Population-based immunogenic peptide identification platform

ABSTRACT

The disclosure relates to methods of identifying fragments of a polypeptide that are immunogenic for a specific human subject, methods of preparing pharmaceutical compositions comprising such polypeptide fragments, pharmaceutical compositions comprising such polypeptide fragments, and methods of treatment using such compositions. The methods comprise identifying a fragment of the polypeptide that binds to multiple HLA of individual subjects.

CROSS-REFERENCE

This application is a continuation of U.S. application Ser. No.15/910,965, filed Mar. 2, 2018, which claims the benefit of priority toEuropean Application No. 17159242.1, filed on Mar. 3, 2017, EuropeanApplication No. 17159243.9, filed on Mar. 3, 2017, and Great BritainApplication No. 1703809.2, filed on Mar. 9, 2017, each of which areincorporated herein by reference in their entireties.

SEQUENCE LISTING

The instant application contains a Sequence Listing which has beensubmitted electronically in ASCII format and is hereby incorporated byreference in its entirety. Said ASCII copy, created Nov. 1, 2021, isnamed “TBL_002C1_SL.txt” and is 64,175 bytes in size.

FIELD

The disclosure relates to methods of predicting whether a polypeptide isimmunogenic for a specific human subject, methods of identifyingfragments of a polypeptide that are immunogenic for a specific humansubject, methods of preparing precision pharmaceutical compositions orkits comprising such polypeptide fragments, human subject-specificpharmaceutical compositions comprising such polypeptide fragments, andmethods of treatment using such compositions.

BACKGROUND

For decades, scientists have assumed that chronic diseases were beyondthe reach of a person's natural defenses. Recently, however, significanttumor regressions observed in individuals treated with antibodies thatblock immune inhibitory molecules have accelerated the field of cancerimmunotherapy. These clinical findings demonstrate that re-activation ofexisting T cell responses results in meaningful clinical benefit forindividuals. These advances have renewed enthusiasm for developingcancer vaccines that induce tumor specific T cell responses.

Despite the promise, current immunotherapy is effective only in afraction of individuals. In addition, most cancer vaccine trials havefailed to demonstrate statistically significant efficacy because of alow rate of tumor regression and antitumor T cell responses inindividuals. Similar failures were reported with therapeutic andpreventive vaccines that sought to include T cell responses in thefields of HIV and allergy. There is a need to overcome the clinicalfailures of immunotherapies and vaccines.

SUMMARY

In antigen presenting cells (APC) protein antigens are processed intopeptides. These peptides bind to human leukocyte antigen molecules(HLAs) and are presented on the cell surface as peptide-HLA complexes toT cells. Different individuals express different HLA molecules anddifferent HLA molecules present different peptides. Therefore, accordingto the state of the art, a peptide, or a fragment of a largerpolypeptide, is identified as immunogenic for a specific human subjectif it is presented by a HLA molecule that is expressed by the subject.In other words, the state of the art describes immunogenic peptides asHLA-restricted epitopes. However, HLA restricted epitopes induce T cellresponses in only a fraction of individuals who express the HLAmolecule. Peptides that activate a T cell response in one individual areinactive in others despite HLA allele matching. Therefore, it wasunknown how an individual's HLA molecules present the antigen-derivedepitopes that positively activate T cell responses.

As provided herein multiple HLA expressed by an individual need topresent the same peptide in order to trigger a T cell response.Therefore the fragments of a polypeptide antigen that are immunogenicfor a specific individual are those that can bind to multiple class I(activate cytotoxic T cells) or class II (activate helper T cells) HLAsexpressed by that individual.

Accordingly, in a first aspect the disclosure provides a method ofpredicting the cytotoxic T cell response rate and/or the helper T cellresponse rate of a specific or target human population to administrationof a polypeptide, or to administration of a pharmaceutical composition,kit or panel of polypeptides comprising one or more polypeptides asactive ingredients, the method comprising

-   -   (i) selecting or defining a relevant model human population        comprising a plurality of subjects each defined by HLA class I        genotype and/or HLA class II genotype;    -   (ii) determining for each subject in the model human population        whether the polypeptide or polypeptides together comprise        -   (a) at least one amino acid sequence that is a T cell            epitope capable of binding to at least two HLA class I            molecules of the subject; and/or        -   (b) at least one amino acid sequence that is a T cell            epitope capable of binding to at least two HLA class II            molecules of the subject; and    -   (iii) predicting        -   A. the cytotoxic T cell response rate of said human            population, wherein a higher proportion of the model human            population meeting the requirements of step (ii)(a) predicts            a higher cytotoxic T cell response rate in said human            population; and/or        -   B. the helper T cell response rate of said human population,            wherein a higher proportion of the model human population            meeting the requirements of step (ii)(b) predicts a higher            helper T cell response rate in said human population.

The disclosure further provides a method of predicting the clinicalresponse rate of a specific or target human population to administrationof a pharmaceutical composition, kit or panel of polypeptides comprisingone or more polypeptides as active ingredients, the method comprising

-   -   (i) selecting or defining a relevant model human population        comprising a plurality of subjects each defined by HLA class I        genotype;    -   (ii) determining        -   (a) for each subject in the model human population whether            the one or more active ingredient polypeptides together            comprise at least two different amino acid sequences each of            which is a T cell epitope capable of binding to at least two            HLA class I molecules of the subject, optionally wherein the            at least two different amino acid sequences are comprised in            the amino acid sequence of two different polypeptide            antigens targeted by the active ingredient polypeptide(s);        -   (b) in the model population the mean number of target            polypeptide antigens that comprise at least one amino acid            sequence that is            -   A. a T cell epitope capable of binding to at least three                HLA class I molecules of the individual subjects of the                model population; and            -   B. comprised in the amino acid sequence of the active                ingredient polypeptide(s); and/or        -   (c) in the model population the mean number of expressed            target polypeptide antigens that comprise at least one amino            acid sequence that is            -   A. a T cell epitope capable of binding to at least three                HLA class I molecules of the individual subjects of the                model population; and            -   B. comprised in the amino acid sequence of the active                ingredient polypeptide(s); and        -   (iii) predicting the clinical response rate of said human            population, wherein a higher proportion of the model human            population meeting the requirements of step (ii)(a), or a            higher mean number of target polypeptides in step (ii)(b),            or a higher mean number of expressed target polypeptides in            step (ii)(c) predicts a higher clinical response rate in            said human population.

The disclosure further provides methods of treatment of a human subjectin need thereof, the method comprising administering to the subject apolypeptide, pharmaceutical composition or kit of the polypeptides of apanel of polypeptides that has been identified or selected based on thepredicted immune or clinical response rate determined as describedabove; their use in a method of treatment of a relevant human subject;and their use in the manufacture of a medicament for treating a relevantsubject.

The disclosure also provides a method of designing or preparing apolypeptide, or a polynucleic acid that encodes a polypeptide, for usein a method of inducing an immune response in a subject of a specific ortarget human population, the method comprising

-   -   (i) selecting or defining        -   (a) a relevant model human population comprising a plurality            of subjects each defined by HLA class I genotype and/or by            HLA class II genotype; and/or        -   (b) a relevant model human population comprising a plurality            of subjects each defined by HLA class I genotype and one            relevant model human population comprising a plurality of            subjects each defined by HLA class II genotype;    -   (ii) identifying a fragment of up to 50 consecutive amino acids        of a target polypeptide antigen that comprises or consists of        -   A. a T cell epitope capable, in a high percentage of the            subjects of a model population selected or defined in            step (i) that is defined by HLA class I genotype, of binding            to at least three HLA class I molecules of the individual            subjects;        -   B. a T cell epitope capable, in a high percentage of the            subjects of a model population selected or defined in            step (i) that is defined by HLA class II genotype, of            binding to at least three HLA class II molecules of the            individual subjects; or        -   C. a T cell epitope capable, in a high percentage of the            subjects of a model population selected or defined in            step (i) that is defined by HLA class I genotype, of binding            to at least three HLA class I molecules of the individual            subjects and a T cell epitope capable, in a high percentage            of the subjects of a model population selected or defined in            step (i) that is defined by HLA class II genotype, of            binding to at least three HLA class II molecules of the            individual subjects;    -   (iii) if the polypeptide fragment selected in step (ii) consists        of an amino acid sequence that is an HLA class I—binding        epitope, optionally selecting a longer fragment of the target        polypeptide antigen, which longer fragment comprises or consists        of an amino acid sequence that        -   D. comprises the fragment selected in step (ii); and        -   E. is an HLA class II molecule-binding T cell epitope            capable, in a high percentage of the subjects of a model            population selected or defined in step (i) that is defined            by HLA class II genotype, of binding to at least three, or            the most possible HLA class II molecules of the individual            subjects; and    -   (iv) designing or preparing a polypeptide, or a polynucleic acid        that encodes a polypeptide that comprises or consists of one or        more polypeptide fragments identified in step (ii) or step        (iii), optionally wherein the polypeptide fragment is flanked at        the N and/or C terminus by additional amino acids that are not        part of the sequence of the target polypeptide antigen.

The disclosure provides a method of inducing an immune response in asubject of a specific or target human population, the method comprisingdesigning or preparing a polypeptide, a panel of polypeptides, apolynucleic acid encoding a polypeptide, or a pharmaceutical compositionor kit for use in said specific or target human population as describedabove and administering the polypeptide(s), polynucleic acid,pharmaceutical composition or the active ingredient polypeptides of thekit to the subject.

The disclosure provides a polypeptide, panel of polypeptides,polynucleic acid, pharmaceutical composition or kit for use in a methodof inducing an immune response in a subject of a specific or targethuman population, wherein the polypeptide, panel of polypeptides,polynucleic acid, pharmaceutical composition or kit is designed orprepared as described above for use in said specific or target humanpopulation, and wherein the composition or kit optionally comprises atleast one pharmaceutically acceptable diluent, carrier, or preservative.

This disclosure provides a pharmaceutical composition, panel ofpolypeptides or kit for use in a method of inducing an immune responsein a human subject, wherein the pharmaceutical composition, panel ofpolypeptides or kit comprises as active ingredients a first and a secondand optionally one or more additional peptides, wherein each peptidecomprises an amino acid sequence that is a T cell epitope capable ofbinding to at least three HLA class I molecules of at least 10% of humansubjects, wherein the T cell epitope of the first, second and optionallyany additional regions are different from each other, and wherein thepharmaceutical composition or kit optionally comprises at least onepharmaceutically acceptable diluent, carrier, or preservative.

The disclosure provides a pharmaceutical composition, panel ofpolypeptides or kit for use in a method of inducing an immune responsein a human subject, wherein the pharmaceutical composition, panel ofpolypeptides or kit comprises an active ingredient polypeptidecomprising a first region and a second region and optionally one or moreadditional regions, wherein each region comprises an amino acid sequencethat is a T cell epitope capable of binding to at least three HLA classI molecules of at least 10% of human subjects, wherein the T cellepitope of the first, second and optionally any additional regions aredifferent from each other, and wherein the pharmaceutical composition orkit optionally comprises at least one pharmaceutically acceptablediluent, carrier, or preservative.

The disclosure provides a pharmaceutical composition, panel ofpolypeptides or kit for use in a method treating a cancer in a subjectin need thereof, wherein the pharmaceutical composition, panel ofpolypeptides or kit comprises as active ingredients a first and a secondpeptide and optionally one or more additional peptides, wherein eachpeptide comprises an amino acid sequence that is an HLA class I-bindingT cell epitope, and wherein for each said T cell epitope at least 10% ofhuman subjects having cancer both

-   -   i. express a tumor associated antigen selected from the antigens        listed in Table 2 or Table 5 below that comprises said T cell        epitope; and    -   ii. have at least three HLA class I molecules capable of binding        to said T cell epitope; wherein said T cell epitope of the        first, second and optionally any additional peptides are        different from each other, and wherein the pharmaceutical        composition or kit optionally comprises at least one        pharmaceutically acceptable diluent, carrier, or preservative.

The disclosure provides a pharmaceutical composition, panel ofpolypeptides or kit for use in a method treating a cancer in a subjectin need thereof, wherein the pharmaceutical composition, panel ofpolypeptides or kit comprises an active ingredient polypeptidecomprising a first and a second region and optionally one or moreadditional regions, wherein each region comprises an amino acid sequencethat is an HLA class I-binding T cell epitope, and wherein for each saidT cell epitope at least 10% of human subjects having cancer both

-   -   (a) express a tumor associated antigen selected from the        antigens listed in Table 2 or Table 5 below that comprises said        T cell epitope; and    -   (b) have at least three HLA class I molecules capable of binding        to said T cell epitope; wherein said T cell epitope of the        first, second and optionally any additional regions are        different from each other, and wherein the pharmaceutical        composition or kit optionally comprises at least one        pharmaceutically acceptable diluent, carrier, or preservative.

The disclosure provides a pharmaceutical composition, panel ofpolypeptides or kit for use in a method treating a cancer selected fromcolorectal, breast, ovarian, melanoma, non-melanoma skin, lung,prostate, kidney, bladder, stomach, liver, cervix uteri, oesophagus,non-Hodgkin lymphoma, leukemia, pancreas, corpus uteri, lip, oralcavity, thyroid, brain, nervous system, gallbladder, larynx, pharynx,myeloma, nasopharynx, Hodgkin lymphoma, testis and Kaposi sarcoma in asubject in need thereof, wherein the pharmaceutical composition, panelof polypeptides or kit comprises as active ingredients a first and asecond peptide and optionally one or more additional polypeptides,wherein each peptide comprises an amino acid sequence that is an HLAclass I-binding T cell epitope, and wherein for each said T cell epitopeat least 10% of human subjects having said cancer both

-   -   (a) express a tumor associated antigen selected from the        antigens listed in Table 2 or Table 5 below that comprises said        T cell epitope; and    -   (b) have at least three HLA class I molecules capable of binding        to said T cell epitope; wherein said T cell epitope of the        first, second and optionally any additional peptides are        different from each other, and wherein the pharmaceutical        composition or kit optionally comprises at least one        pharmaceutically acceptable diluent, carrier, or preservative.

The disclosure provides a pharmaceutical composition, panel ofpolypeptides or kit for use in a method treating a cancer selected fromcolorectal, breast, ovarian, melanoma, non-melanoma skin, lung,prostate, kidney, bladder, stomach, liver, cervix uteri, oesophagus,non-Hodgkin lymphoma, leukemia, pancreas, corpus uteri, lip, oralcavity, thyroid, brain, nervous system, gallbladder, larynx, pharynx,myeloma, nasopharynx, Hodgkin lymphoma, testis and Kaposi sarcoma in asubject in need thereof, wherein the pharmaceutical composition, panelof polypeptides or kit comprises an active ingredient polypeptidecomprising a first and a second region and optionally one or moreadditional regions, wherein each region comprises an amino acid sequencethat is an HLA class I-binding T cell epitope, and wherein for each saidT cell epitope at least 10% of human subjects having said cancer both

-   -   (a) express a tumor associated antigen selected from the        antigens listed in Table 2 or Table 5 below that comprises said        T cell epitope; and    -   (b) have at least three HLA class I molecules capable of binding        to said T cell epitope; wherein said T cell epitope of the        first, second and optionally any additional polypeptides are        different from each other, and wherein the pharmaceutical        composition or kit optionally comprises at least one        pharmaceutically acceptable diluent, carrier, or preservative.

The disclosure provides a method of treatment of a human subject in needthereof, the method comprising administering to the subject apolypeptide, a panel of polypeptides, a pharmaceutical composition orthe active ingredient polypeptides of a kit described above, wherein thesubject has been determined to express at least three HLA class Imolecules and/or at least three HLA class II molecules capable ofbinding to the polypeptide or to one or more of the active ingredientpoypeptides of the pharmaceutical composition or kit.

In a further aspect the invention provides a system comprising

-   -   (a) a storage module configured to store data comprising the        class I and/or class II HLA genotypes of each subject of a model        population of human subjects; and the amino acid sequence of one        or more test polypeptides; wherein the model population is        representative of a test target human population; and    -   (b) a computation module configured to identify and/or quantify        the amino acid sequences in the one or more test polypeptides        that are capable of binding to multiple class I HLA molecules of        each subject in the model population and/or the amino acid        sequences in the one or more test polypeptides that are capable        of binding to multiple class II HLA molecules of each subject in        the model population.

Provided herein in certain embodiments are pharmaceutical compositionsfor treatment of a disease or disorder in a subject of a target humanpopulation, comprising one or more polypeptides, each comprising atleast a first region and a second region, (a) the first region being of10-50 amino acids in length comprising a first amino acid sequence thatis a T cell epitope that binds at least three HLA class I molecules ofat least 10% of subjects in the target population and/or at least threeHLA class II molecules of at least 10% of subjects in the targetpopulation; and (b) the second region being of 10-50 amino acids inlength comprising a second amino acid sequence that is a T cell epitopethat binds at least three HLA class I molecules of at least 10% ofsubjects in the target population and/or at least three HLA class IImolecules of at least 10% of subjects in the target population; whereinthe amino acid sequence of the T cell epitope of each of first andsecond regions comprise different sequences. In some embodiments, thecomposition comprises at least 2, at least 3, at least 4, at least 5, atleast 6, at least 7, at least 8, at least 9, at least 10, at least 11,or at least 12 different polypeptides. In some embodiments, thecomposition comprises 2-40 different polypeptides. In some embodiments,the T cell epitope that binds at least three HLA class I molecules of atleast 10% of subjects in the target population comprises 7 to 11 aminoacids, and/or the T cell epitope that binds at least three HLA class IImolecules of at least 10% of subjects in the target population comprises13 to 17 amino acids. In some embodiments, the first region of 10-50amino acids in length is from an antigen; and the second region of 10-50amino acids in length is from a same or different antigen. In someembodiments, the epitopes of the first and second regions are from asingle antigen. In some embodiments, the epitopes of the first andsecond regions are from two or more different antigens. In someembodiments, the antigen is a cancer-associated antigen, atumor-associated antigen, or an antigen expressed by a target pathogenicorganism, an antigen expressed by a virus, an antigen expressed by abacterium, an antigen expressed by a fungus, an antigen associated withan autoimmune disorder, or is an allergen. In some embodiments, theantigen is selected from the antigens listed in Tables 2 to 7. In someembodiments, the two or more different antigens are selected from theantigens listed in Tables 2 to 7 and/or different cancer associatedantigens. In some embodiments, one or more of the antigens are cancertestis antigens (CTAs). In some embodiments, the one or morepolypeptides further comprise up to 10 amino acids flanking the T cellepitope that are not part of a consecutive sequence flanking the epitopein a corresponding antigen. In some embodiments, the one or morepolypeptides have been screened to eliminate substantially allneoepitopes that span a junction between the first region and secondregion and that (i) corresponds to a fragment of a human polypeptideexpressed in healthy cells; (ii) is a T cell epitope capable of bindingto at least three HLA class I molecules of at least 10% of subjects inthe target population; or (iii) meets both requirements (i) and (ii). Insome embodiments, the target population is cancer patients and whereineach of the first region and second region comprises an amino acidsequence that is an HLA class I-binding T cell epitope, and wherein foreach T cell epitope, at least 10% of subjects in the target populationexpress a tumor associated antigen selected from the antigens listed inTable 2 that comprises the T cell epitope; and at least 10% of subjectsin the target population have at least three HLA class I moleculescapable of binding to the T cell epitope; wherein the T cell epitope ofthe first and second regions are different from each other. In someembodiments, the composition further comprises a pharmaceuticallyacceptable adjuvant, diluent, carrier, preservative, or combinationthereof. In some embodiments, the adjuvant is selected from the groupconsisting of Montanide ISA-51, QS-21, GM-CSF, cyclophosamide, bacillusCalmette-Guerin (BCG), corynbacterium parvum, levamisole, azimezone,isoprinisone, dinitrochlorobenezene (DNCB), keyhole limpet hemocyanins(KLH), Freunds adjuvant (complete), Freunds adjuvant (incomplete),mineral gels, aluminum hydroxide (Alum), lysolecithin, pluronic polyols,polyanions, oil emulsions, dinitrophenol, diphtheria toxin (DT), andcombinations thereof.

Disclosed herein, in certain embodiments, are kits comprising, one ormore separate containers each container comprising: (i) one or morepolypeptides comprising at least a first region and a second region, (a)the first region of 10-50 amino acids in length comprising a first aminoacid sequence that is a T cell epitope that binds at least three HLAclass I molecules of at least 10% of subjects in the target populationand/or at least three HLA class II molecules of at least 10% of subjectsin the target population; and (b) the second region of 10-50 amino acidsin length comprising a second amino acid sequence that is a T cellepitope that binds at least three HLA class I molecules of at least 10%of subjects in the target population and/or at least three HLA class IImolecules of at least 10% of subjects in the target population; whereinthe amino acid sequence of the T cell epitope of each of first andsecond regions comprise different sequences and (ii) a pharmaceuticallyacceptable adjuvant, diluent, carrier, preservative, or combinationthereof. In some embodiments, the kit further comprises a packageinsert.

Disclosed herein, in certain embodiments, are pharmaceuticalcompositions comprising: one or more nucleic acid molecules expressingone or more polypeptides comprising at least a first region and a secondregion, (a) the first region of 10-50 amino acids in length comprising afirst amino acid sequence that is a T cell epitope that binds at leastthree HLA class I molecules of at least 10% of subjects in the targetpopulation and/or at least three HLA class II molecules of at least 10%of subjects in the target population; and (b) the second region of 10-50amino acids in length comprising a second amino acid sequence that is aT cell epitope that binds at least three HLA class I molecules of atleast 10% of subjects in the target population and/or at least three HLAclass II molecules of at least 10% of subjects in the target population;wherein the amino acid sequence of the T cell epitope of each of firstand second regions comprise different sequences.

Disclosed herein, in certain embodiments are methods of preparing apolypeptide, or a polynucleic acid that encodes a polypeptide, for usein a method of inducing an immune response in a subject of a targethuman population, the method comprising:

-   -   (i) selecting:        -   (a) a relevant model human population comprising a plurality            of subjects each defined by HLA class I genotype and/or by            HLA class II genotype; or        -   (b) one relevant model human population comprising a            plurality of subjects each defined by HLA class I genotype            and one relevant model human population comprising a            plurality of subjects each defined by HLA class II genotype;    -   (ii) identifying a fragment of up to 50 consecutive amino acids        of an antigen that comprises:        -   (a) a T cell epitope capable, in a high percentage of            subjects of the model population selected in step (i) that            is defined by HLA class I genotype, of binding to at least            three HLA class I molecules of individual subjects of the            model population;        -   (b) a T cell epitope capable, in a high percentage of            subjects of the model population selected in step (i) that            is defined by HLA class II genotype, of binding to at least            three HLA class II molecules of individual subjects of the            model population; or        -   (c) a T cell epitope capable, in a high percentage of            subjects of the model population selected in step (i) that            is defined by HLA class I genotype, of binding to at least            three HLA class I molecules of individual subjects of the            model population and a T cell epitope capable, in a high            percentage of subjects of the model population selected in            step (i) that is defined by HLA class II genotype, of            binding to at least three HLA class II molecules of            individual subjects of the model population; and    -   (iii) preparing a polypeptide, or a polynucleic acid that        encodes a polypeptide that comprises one or more fragments        identified in step (ii). In some embodiments, the method further        comprises prior to step (iii), selecting a longer fragment of        the antigen if the fragment selected in step (ii) is an HLA        class I—binding epitope, which longer fragment comprises an        amino acid sequence that (a) comprises the fragment selected in        step (ii); and (b) is an HLA class II molecule-binding T cell        epitope capable, in a high percentage of subjects of the model        population selected in step (i) that is defined by HLA class II        genotype, of binding to at least three, or the most possible HLA        class II molecules of individual subjects of the model        population. In some embodiments, the method further comprises        prior to step (iii), repeating steps (i) to (ii) to identify on        or more additional amino acid sequences of up to 50 consecutive        amino acids of the same or a different polypeptide to the first        amino acid sequence.

Disclosed herein in certain embodiments are methods of inducing animmune response in a subject of a target human population, the methodcomprising, administering to the subject a pharmaceutical compositioncomprising one or more polypeptides comprising at least a first regionand a second region, (a) the first region being of 10-50 amino acids inlength comprising a first amino acid sequence that is a T cell epitopethat binds at least three HLA class I molecules of at least 10% ofsubjects in the target population and/or at least three HLA class IImolecules of at least 10% of subjects in the target population; and (b)the second region being of 10-50 amino acids in length comprising asecond amino acid sequence that is a T cell epitope that binds at leastthree HLA class I molecules of at least 10% of subjects in the targetpopulation and/or at least three HLA class II molecules of at least 10%of subjects in the target population; wherein the amino acid sequence ofthe T cell epitope of each of first and second regions comprisedifferent sequences. In some embodiments, the method further comprisesprior to the administering step, determining if the subject is likely tohave an have a clinical response to administration of a pharmaceuticalcomposition by (i) assaying a biological sample of the subject todetermine HLA genotype of the subject; (ii) determining that thepharmaceutical composition comprises two or more sequences that are a Tcell epitope capable of binding to at least three HLA class I moleculesof the subject; and (iii) determining the probability that a tumor ofthe subject expresses one or more antigen corresponding to the T cellepitopes identified in step (ii) using population expression data foreach antigen, to identify the likelihood of the subject to have aclinical response to administration of the pharmaceutical composition.In some embodiments, the first region of 10-50 amino acids in length isfrom an antigen; and the second region of 10-50 amino acids in length isfrom a same or different antigen. In some embodiments, the epitopes ofthe first and second regions are from two or more different antigens. Insome embodiments, the antigen is a cancer-associated antigen, atumor-associated antigen, or an antigen expressed by a target pathogenicorganism, an antigen expressed by a virus, an antigen expressed by abacterium, an antigen expressed by a fungus, an antigen associated withan autoimmune disorder, or is an allergen. In some embodiments, the Tcell epitope that binds at least three HLA class I molecules of at least10% of subjects in the target population comprises 7 to 11 amino acids,and/or the T cell epitope that binds at least three HLA class IImolecules of at least 10% of subjects in the target population comprises13 to 17 amino acids.

Disclosed herein in certain embodiments are pharmaceutical compositionsfor treatment of a disease or disorder in a subject of a target humanpopulation, comprising (a) at least two polypeptides, each of the atleast two polypeptides being 10-50 amino acids in length comprising anamino acid sequence that is a T cell epitope that binds at least threeHLA class I molecules of at least 10% of subjects in the targetpopulation, and/or at least three HLA class II molecules of at least 10%of subjects in the target population, wherein the amino acid sequence ofthe T cell epitope of each of the at least two polypeptides aredifferent from each other; and (b) a pharmaceutically-acceptableadjuvant. In some embodiments, the composition comprises at least 3, atleast 4, at least 5, at least 6, at least 7, at least 8, at least 9, atleast 10, at least 11, or at least 12 different polypeptides. In someembodiments, the composition comprises 3-40 different polypeptides. Insome embodiments, the T cell epitope that binds at least three HLA classI molecules of at least 10% of subjects in the target populationcomprises 7 to 11 amino acids, and/or the T cell epitope that binds atleast three HLA class II molecules of at least 10% of subjects in thetarget population comprises 13 to 17 amino acids. In some embodiments,the epitopes of the amino acid sequences of the at least twopolypeptides are from a single antigen. In some embodiments, theepitopes of the amino acid sequences of the at least two polypeptidesare from two or more different antigens. In some embodiments, theantigen is a cancer-associated antigen, a tumor-associated antigen, oran antigen expressed by a target pathogenic organism, an antigenexpressed by a virus, an antigen expressed by a bacterium, an antigenexpressed by a fungus, an antigen associated with an autoimmunedisorder, or is an allergen. In some embodiments, the antigen isselected from the antigens listed in Tables 2 to 7. In some embodiments,the two or more different antigens are selected from the antigens listedin Tables 2 to 7 and/or different cancer associated antigens. In someembodiments, one or more of the antigens are cancer testis antigens(CTAs). In some embodiments, each of the at least two polypeptides being10-50 amino acids in length is from an antigen a same or differentantigen. In some embodiments, the at least two different polypeptidesfurther comprise up to 10 amino acids flanking the T cell epitope thatare not part of a consecutive sequence flanking the epitope in acorresponding antigen. In some embodiments, two of the at least twopolypeptides are arranged end to end or overlapping in a joinedpolypeptide. In some embodiments, two or more different joinedpolypeptides, wherein the two or more different joined polypeptidescomprise different epitopes from each other. In some embodiments, thejoined polypeptides have been screened to eliminate substantially allneoepitopes that span a junction between the two polypeptides and that(i) corresponds to a fragment of a human polypeptide expressed inhealthy cells; (ii) is a T cell epitope capable of binding to at leastthree HLA class I molecules of at least 10% of subjects in the targetpopulation; or (iii) meets both requirements (i) and (ii). In someembodiments, the target population is cancer patients and wherein eachpolypeptide comprises an amino acid sequence that is an HLA classI-binding T cell epitope, and wherein for each T cell epitope, at least10% of subjects in the target population express a tumor associatedantigen selected from the antigens listed in Table 2 that comprises theT cell epitope; and at least 10% of subjects in the target populationhave at least three HLA class I molecules capable of binding to the Tcell epitope; wherein the T cell epitope of the at least twopolypeptides are different from each other. In some embodiments, thecomposition further comprises a pharmaceutically acceptable diluent,carrier, preservative, or combination thereof. In some embodiments, theadjuvant is selected from the group consisting of Montanide ISA-51,QS-21, GM-CSF, cyclophosamide, bacillus Calmette-Guerin (BCG),corynbacterium parvum, levamisole, azimezone, isoprinisone,dinitrochlorobenezene (DNCB), keyhole limpet hemocyanins (KLH), Freundsadjuvant (complete), Freunds adjuvant (incomplete), mineral gels,aluminum hydroxide (Alum), lysolecithin, pluronic polyols, polyanions,oil emulsions, dinitrophenol, diphtheria toxin (DT), and combinationsthereof.

Disclosed herein in certain embodiments are pharmaceutical compositionsfor treatment of a disease or disorder in a subject of a target humanpopulation, comprising (a) a polypeptide of 10-50 amino acids in lengthand comprising a T cell epitope that binds at least three HLA class Imolecules of at least 10% of subjects in the target population and/or atleast three HLA class II molecules of at least 10% of subjects in thetarget population; and (b) a pharmaceutically-acceptable adjuvant. Insome embodiments, the composition comprises at least 2, at least 3, atleast 4, at least 5, at least 6, at least 7, at least 8, at least 9, atleast 10, at least 11, or at least 12 different polypeptides, each ofthe different polypeptides being 10-50 amino acids in length comprisinga T cell epitope that binds at least three HLA class I molecules of atleast 10% of subjects in the target population and/or at least three HLAclass II molecules of at least 10% of subjects in the target population,wherein the amino acid sequence of the T cell epitope of each of thedifferent polypeptides are different from each other. In someembodiments, the composition comprises 2-40 different polypeptides. Insome embodiments, the T cell epitope that binds at least three HLA classI molecules of the subject comprises 7 to 11 amino acids, and/or the Tcell epitope that binds at least three HLA class II molecules comprises13 to 17 amino acids. In some embodiments, the composition comprises atleast two different polypeptides, wherein the epitopes of the at leasttwo different polypeptides are from a single antigen. In someembodiments, the composition comprises at least two differentpolypeptides, wherein the epitopes of the at least two differentpolypeptides are from two or more different antigens. In someembodiments, the antigen is an antigen expressed by a cancer cell, aneoantigen expressed by a cancer cell, a cancer-associated antigen, atumor-associated antigen, or an antigen expressed by a target pathogenicorganism, an antigen expressed by a virus, an antigen expressed by abacterium, an antigen expressed by a fungus, an antigen associated withan autoimmune disorder, or is an allergen. In some embodiments, theantigen is selected from the antigens listed in Tables 2 to 7. In someembodiments, the composition comprises at least two differentpolypeptides, wherein two of the polypeptides are arranged end to end oroverlapping in a joined polypeptide. In some embodiments, the adjuvantis selected from the group consisting of Montanide ISA-51, QS-21,GM-CSF, cyclophosamide, bacillus Calmette-Guerin (BCG), corynbacteriumparvum, levamisole, azimezone, isoprinisone, dinitrochlorobenezene(DNCB), keyhole limpet hemocyanins (KLH), Freunds adjuvant (complete),Freunds adjuvant (incomplete), mineral gels, aluminum hydroxide (Alum),lysolecithin, pluronic polyols, polyanions, oil emulsions,dinitrophenol, diphtheria toxin (DT), and combinations thereof. In someembodiments, the composition comprises at least two differentpolypeptides, wherein two of the at least two polypeptides are arrangedend to end or overlapping in a joined polypeptide. In some embodiments,the composition comprises two or more different joined polypeptides,wherein the two or more different joined polypeptides comprise differentepitopes from each other. In some embodiments, the joined polypeptideshave been screened to eliminate substantially all neoepitopes that spana junction between the two polypeptides and that (i) corresponds to afragment of a human polypeptide expressed in healthy cells of thesubject; (ii) is a T cell epitope capable of binding to at least two HLAclass I molecules of the subject; or (iii) meets both requirements (i)and (ii). In some embodiments, the at least two polypeptides do notcomprise any amino acid sequences that (i) correspond to a fragment of ahuman polypeptide expressed in healthy cells; or (ii) correspond to afragment of a human polypeptide expressed in healthy cells and is a Tcell epitope capable of binding to at least two HLA class I molecules ofthe subject.

Disclosed herein in certain embodiments are methods of identifying andtreating a subject of a target population of cancer patients who willlikely have a clinical response to administration of a pharmaceuticalcomposition of the disclosure, the method comprising, (i) assaying abiological sample of the subject to determine HLA genotype of thesubject; (ii) determining that the pharmaceutical composition comprisestwo or more sequences that are a T cell epitope capable of binding to atleast three HLA class I molecules of the subject; (iii) determining theprobability that a tumor of the subject expresses one or more antigencorresponding to the T cell epitopes identified in step (ii) usingpopulation expression data for each antigen, to identify the likelihoodof the subject to have a clinical response to administration of thepharmaceutical composition; and (iv) administering the composition ofthe disclosure to the identified subject. In some embodiments, themethod further comprises prior to the administering step, assaying atumor sample from the subject to determine that the three or morepeptides of the pharmaceutical composition comprise two or moredifferent amino acid sequences each of which is a fragment of acancer-associated antigen expressed by cancer cells of the subject asdetermined in step (i); and a T cell epitope capable of binding to atleast three HLA class I molecules of the subject; and confirming thesubject as likely to have a clinical response to the method oftreatment. In some embodiments, the composition comprises at least 2, atleast 3, at least 4, at least 5, at least 6, at least 7, at least 8, atleast 9, at least 10, at least 11, or at least 12 differentpolypeptides. In some embodiments, the composition comprises 2-40different polypeptides. In some embodiments, the T cell epitope thatbinds at least three HLA class I molecules of at least 10% of subjectsin the target population comprises 7 to 11 amino acids, and/or the Tcell epitope that binds at least three HLA class II molecules of atleast 10% of subjects in the target population comprises 13 to 17 aminoacids. In some embodiments, the first region of 10-50 amino acids inlength is from an antigen; and the second region of 10-50 amino acids inlength is from a same or different antigen. In some embodiments, theepitopes of the first and second regions are from a single antigen. Insome embodiments, the epitopes of the first and second regions are fromtwo or more different antigens. In some embodiments, the antigen is acancer-associated antigen or a tumor-associated antigen. In someembodiments, the antigen is selected from the antigens listed in Table2. In some embodiments, the two or more different antigens are selectedfrom the antigens listed in Table 2 and/or different cancer associatedantigens. In some embodiments, one or more of the antigens are cancertestis antigens (CTAs). In some embodiments, the one or morepolypeptides further comprise up to 10 amino acids flanking the T cellepitope that are not part of a consecutive sequence flanking the epitopein a corresponding antigen. In some embodiments, the one or morepolypeptides have been screened to eliminate substantially allneoepitopes that span a junction between the first region and secondregion and that (i) corresponds to a fragment of a human polypeptideexpressed in healthy cells; (ii) is a T cell epitope capable of bindingto at least three HLA class I molecules of at least 10% of subjects inthe target population; or (iii) meets both requirements (i) and (ii). Insome embodiments, the target population is cancer patients and whereineach of the first region and second region comprises an amino acidsequence that is an HLA class I-binding T cell epitope, and wherein foreach T cell epitope, at least 10% of subjects in the target populationexpress a tumor associated antigen selected from the antigens listed inTable 2 that comprises the T cell epitope; and at least 10% of subjectsin the target population have at least three HLA class I moleculescapable of binding to the T cell epitope; wherein the T cell epitope ofthe first and second regions are different from each other. In someembodiments, the composition further comprises a pharmaceuticallyacceptable adjuvant, diluent, carrier, preservative, or combinationthereof. In some embodiments, the adjuvant is selected from the groupconsisting of Montanide ISA-51, QS-21, GM-CSF, cyclophosamide, bacillusCalmette-Guerin (BCG), corynbacterium parvum, levamisole, azimezone,isoprinisone, dinitrochlorobenezene (DNCB), keyhole limpet hemocyanins(KLH), Freunds adjuvant (complete), Freunds adjuvant (incomplete),mineral gels, aluminum hydroxide (Alum), lysolecithin, pluronic polyols,polyanions, oil emulsions, dinitrophenol, diphtheria toxin (DT), andcombinations thereof.

Disclosed herein in certain embodiments are kits comprising: a firstcomposition comprising (i) a first polypeptide of 10-50 amino acids inlength and comprising a T cell epitope that binds at least three HLAclass I molecules of at least 10% of subjects in the target populationand/or at least three HLA class II molecules of at least 10% of subjectsin the target population; and (ii) a pharmaceutically-acceptableadjuvant; and a second composition comprising (i) a second polypeptideof 10-50 amino acids in length and comprising a T cell epitope thatbinds at least three HLA class I molecules of at least 10% of subjectsin the target population and/or at least three HLA class II molecules ofat least 10% of subjects in the target population; and (ii) apharmaceutically-acceptable adjuvant, wherein the first and secondpolypeptides comprise different T cell epitopes. In some embodiments,the first composition and/or the second composition comprise one or moreadditional polypeptides, wherein each additional polypeptide being of10-50 amino acids in length comprising an amino acid sequence that is aT cell epitope that binds at least three HLA class I molecules of atleast 10% of subjects in the target population and/or at least three HLAclass II molecules of at least 10% of subjects in the target population,wherein the amino acid sequences comprise different T cell epitopes.

Disclosed herein in certain embodiments are methods of identifying andtreating a subject of a target population of cancer patients who willlikely have an immune response to administration of a pharmaceuticalcomposition of the disclosure, the method comprising, (i) assaying abiological sample of the subject to determine HLA genotype of thesubject; (ii) determining that the pharmaceutical composition comprisestwo or more sequences that are a T cell epitope capable of binding to atleast three HLA class I molecules of the subject; (iii) administeringthe composition of the disclosure to the identified subject.

Disclosed herein in certain embodiments are pharmaceutical compositionscomprising: a nucleic acid molecule expressing two or more polypeptides,each polypeptide being 10-50 amino acids in length comprising a T cellepitope that binds at least three HLA class I molecules of at least 10%of subjects in the target population and/or at least three HLA class IImolecules of at least 10% of subjects in the target population, whereineach of the two or more polypeptides comprises a different T cellepitope, wherein the polypeptides do not comprise amino acid sequencesthat are adjacent to each other in a corresponding antigen.

The disclosure will now be described in more detail, by way of exampleand not limitation, and by reference to the accompanying drawings. Manyequivalent modifications and variations will be apparent, to thoseskilled in the art when given this disclosure. Accordingly, theexemplary embodiments of the disclosure set forth are considered to beillustrative and not limiting. Various changes to the describedembodiments may be made without departing from the scope of thedisclosure. All documents cited herein, whether supra or infra, areexpressly incorporated by reference in their entirety.

The present disclosure includes the combination of the aspects andpreferred features described except where such a combination is clearlyimpermissible or is stated to be expressly avoided. As used in thisspecification and the appended claims, the singular forms “a”, “an”, and“the” include plural referents unless the content clearly dictatesotherwise. Thus, for example, reference to “a peptide” includes two ormore such peptides.

Section headings are used herein for convenience only and are not to beconstrued as limiting in any way.

DESCRIPTION OF THE FIGURES

FIG. 1—ROC curve of HLA restricted PEPI biomarkers.

FIG. 2—ROC curve of ≥1 PEPI3+ Test for the determination of thediagnostic accuracy.

FIGS. 3A-B—Distribution of HLA class I PEPI3+ compared to CD8+ T cellresponses measured by a state of art assay among peptide pools used inthe CD8+ T cell response assays. FIG. 3A: HLA class I restrictedPEPI3+s. The 90% Overall Percent of Agreement (OPA) among the T cellresponses and PEPI3+ peptides demonstrate the utility of the disclosedpeptides for prediction of vaccine induced T cell response set ofindividuals. FIG. 3B: Class I HLA restricted epitopes (PEPI1+). The OPAbetween predicted epitopes and CD8+ T cell responses was 28% (notstatistically significant). Darkest grey: True positive (TP), bothpeptide and T cell responses were detected; Light grey: False negative(FN), only T cell responses were detected; Lightest grey: False positive(FP), only peptide were detected; Dark grey: True negative (TN): neitherpeptides nor T cell responses were detected.

FIGS. 4A-B—Distribution of HLA class II PEPIs compared to CD4+ T cellresponses measured by a state of art assay among peptide pools used inthe assays. FIG. 4A: HLA class II restricted PEPI4+s. 67% OPA betweenPEPI4+ and CD4+ T-cell responses (p=0.002). FIG. 4B: The class II HLArestricted epitopes. OPA between class II HLA restricted epitopes andCD4+ T cell responses was 66% (not statistically significant). Darkestgrey: True positive (TP), both peptide and T cell responses weredetected; Light grey: False negative (FN), only T cell responses weredetected; Lightest grey: False positive (FP), only peptide weredetected; Dark grey: True negative (TN): neither peptides nor T cellresponses were detected.

FIGS. 5A-D—Multiple HLA binding peptides that define the HPV-16 LPVvaccine specific T cell response set of 18 VIN-3 and 5 cervical cancerpatients. HLA class I restricted PEPI3 counts (FIGS. 5A and 5B) and HLAclass II restricted PEPI3 counts (FIGS. 5C and 5D) derived from LPVantigens of each patient. Light grey: immune responders measured aftervaccination in the clinical trial; Dark grey: Immune non-respondersmeasured after vaccination in the clinical trial. Results show that ≥3HLA class I binding peptides predict the CD8+ T cell reactivity and ≥4HLA class II binding peptides predict the CD4+ T cell reactivity.

FIG. 6—The multiple HLA class I binding peptides that define the HPVvaccine specific T cell response set of 2 patients. Panel A: Four HPVantigens in the HPV vaccine. Boxes represent the length of the aminoacid sequences from the N terminus to the C terminus. Panel B: Processto identify the multiple HLA binding peptides of two patients: HLAsequences of the patients labelled as 4-digit HLA genotype right fromthe patient's ID. The location of the 1^(st) amino acid of the 54 and 91epitopes that can bind to the patient 12-11 and patient 14-5 HLAs(PEPI1+) respectively are depicted with lines. PEPI2 represents thepeptides selected from PEPI1+s that can bind to multiple HLAs of apatient (PEPI2+). PEPI3 represent peptides that can bind to ≥3 HLAs of apatient (PEPI3+). PEPI4 represent peptides that can bind to ≥4 HLAs of apatient (PEPI4+). PEPI5 represent peptides that can bind to ≥5 HLAs of apatient (PEPI5+). PEPI6 represent peptides that can bind to 6 HLAs of apatient (PEPI6). Panel C: The DNA vaccine specific PEPI3+ set of twopatients characterizes their vaccine specific T cell responses.

FIG. 7—Correlation between the ≥1 PEPI3+ Score and CTL response rates ofpeptide targets determined in clinical trials. FIG. 7 discloses SEQ IDNOS 103-106, 108, 107, 109-115, respectively, in order of appearance.

FIG. 8—Correlation between the ≥1 PEPI3+ Score and the clinical ImmuneResponse Rate (IRR) of immunotherapy vaccines. Dashed lines: 95%confidence band.

FIG. 9—Correlation between the ≥2 PEPI3+ Score and Disease Control Rate(DCR) of immunotherapy vaccines. Dashed lines: 95% confidence band.

FIG. 10—HLA map of the Rindopepimut on the HLA alleles of the subjectsin the Model Population. FIG. 10 discloses SEQ ID NO: 189.

FIGS. 11A-B—Probability of vaccine antigen expression in the XYZpatient's tumor cells. There is over 95% probability that 5 out of the12 target antigens in the vaccine regimen is expressed in the patient'stumor. Consequently, the 12 peptide vaccines together can induce immuneresponses against at least 5 ovarian cancer antigens with 95%probability (AGP95). It has 84% probability that each peptide willinduce immune responses in the XYZ patient. AGP50 is the mean (expectedvalue)=7.9 (it is a measure of the effectiveness of the vaccine inattacking the tumor of XYZ patient).

FIG. 12—MRI findings of patient XYZ treated with personalised (PIT)vaccine. This late stage, heavily pretreated ovarian cancer patient hadan unexpected objective response after the PIT vaccine treatment. TheseMRI findings suggest that PIT vaccine in combination with chemotherapysignificantly reduced her tumor burden. The patient now continues thePIT vaccine treatment.

FIGS. 13A-B—Probability of vaccine antigen expression in the ABCpatient's tumor cells. There is over 95% probability that 4 out of the13 target antigens in the vaccine is expressed in the patient's tumor.Consequently, the 12 peptide vaccines together can induce immuneresponses against at least 4 breast cancer antigens with 95% probability(AGP95). It has 84% probability that each peptide will induce immuneresponses in the ABC patient. AGP50 is the mean (expected value) of thediscrete probability distribution=6.45 (it is a measure of theeffectiveness of the vaccine in attacking the tumor of ABC patient).

FIG. 14—Peptide hotspot analysis example: PRAME antigen hotspot on 433patients of the Model Population. On the y axis are the 433 patients ofthe Model Population, on the x axis is the amino acid sequence of thePRAME antigen (CTA). Each data point represents a PEPI presented by ≥3HLA class I of one patient starting at the specified amino acidposition. The two most frequent PEPIs (called bestEPIs) of the PRAMEantigen are highlighted in dark gray (peptide hotspots=PEPI Hotspots).

FIG. 15—CTA Expression Curve calculated by analyzing expressionfrequency data of tumor specific antigens (CTAs) in human breast cancertissues. (No cell line data were included.)

FIGS. 16A-B—Antigen expression distribution for breast cancer based onthe calculation of multi-antigen responses from expression frequenciesof the selected 10 different CTAs. FIG. 16A: non-cumulative distributionto calculate the expected value for the number of expressed antigens(AG50). This value shows that probably 6.14 vaccine antigens will beexpressed by breast tumor cells. FIG. 16B: cumulative distribution curveof the minimum number of expressed antigens (CTA expression curve). Thisshows that minimum 4 vaccine antigens will be expressed with 95%probability in breast cancer cell (AG95).

FIGS. 17A-B—PEPI representing antigens: breast cancer vaccine-specificCTA antigens with ≥1 PEPI, called as “AP”) distribution within the ModelPopulation (n=433) for breast cancer vaccine. FIG. 17A: non-cumulativedistribution of AP where the average number of APs is: AP50=5.30,meaning that in average almost 6 CTAs will have PEPIs in the ModelPopulation.

FIG. 17B: cumulative distribution curve of the minimum number of APs inthe Model Population (n=433). This shows that at least one vaccineantigen will have PEPIs in 95% of the Model Population (n=433) (AP95=1).

FIGS. 18A-B—PEPI represented expressed antigen (breast cancervaccine-specific CTA antigens expressed by the tumor, for which ≥1 PEPIis predicted, called as “AGP”) distribution within the model population(n=433) calculated with CTA expression rates for breast cancer. FIG.18A: non-cumulative distribution of AGP where the expected value fornumber expressed CTAs represented by PEPI is AGP50=3.37. AGP50 is ameasure of the effectiveness of the disclosed breast cancer vaccine inattacking breast tumor in an unselected patient population. AGP50=3.37means that at least 3 CTAs from the vaccine will probably be expressedby the breast tumor cells and present PEPIs in the Model Population.FIG. 18B: cumulative distribution curve of the minimum number of AGPs inthe Model Population (n=433) shows that at least 1 of the vaccine CTAswill present PEPIs in 92% of the population and the remaining 8% of thepopulation will likely have no AGP at all (AGP95=0, AGP92=1).

FIG. 19—CTA Expression Curve calculated by analyzing expressionfrequency data of tumor specific antigens (CTAs) in human colorectalcancer tissues. (No cell line data were included.)

FIGS. 20A-B—Antigen expression distribution for colorectal cancer basedon the calculation of multi-antigen responses from expressionfrequencies of the selected 7 different CTAs. FIG. 20A: non-cumulativedistribution to calculate the expected vale for the number of expressedvaccine antigens in colorectal cancers (AG50). This value shows thatprobably 4.96 vaccine antigens will be expressed by colorectal tumorcells. FIG. 20B: cumulative distribution curve of the minimum number ofexpressed antigens (CTA expression curve). This shows that minimum 3antigens will be expressed with 95% probability in the colorectal cancercell (AG95).

FIGS. 21A-B—PEPI represented antigen (colorectal cancer vaccine-specificCTA antigens for which ≥1 PEPI is predicted. Called as “AP”)distribution within the model population (n=433) for colorectal cancer.FIG. 21A: non-cumulative distribution of AP where the average number ofAPs is: AP50=4.73, meaning that in average 5 CTAs will be represented byPEPIs in the model population FIG. 21B: cumulative distribution curve ofthe minimum number of APs in the model population (n=433). This showsthat 2 or more antigens will be represented by PEPIs in 95% of the modelpopulation (n=433) (AP95=2).

FIGS. 22A-B—PEPI represented expressed antigen (colorectal cancervaccine-specific CTA antigens expressed by the tumor, for which ≥1 PEPIis predicted. Called as “AGP”) distribution within the model population(n=433) calculated with CTA expression rates for colorectal cancer. FIG.22A: non-cumulative distribution of AGP where the expected value fornumber expressed CTAs represented by PEPI is AGP50=2.54. AGP50 is ameasure of the effectiveness of the disclosed colorectal cancer vaccinein attacking colorectal tumors in an unselected patient population.AGP50=2.54 means that at least 2-3 CTAs from the vaccine will probablybe expressed by the colorectal tumor cells and present PEPIs in theModel Population. FIG. 22B: cumulative distribution curve of the minimumnumber of AGPs in the Model Population (n=433) shows that at least 1 ofthe vaccine CTAs will be expressed and also present PEPIs in 93% of thepopulation (AGP93=1).

FIG. 23—Schematic showing exemplary positions of amino acids inoverlapping HLA class I- and HLA class-II binding epitopes in a 30-merpeptide.

FIGS. 24A-B—Antigenicity of PolyPEPI1018 CRC Vaccine in a generalpopulation. The antigenicity of PolyPEPI1018 in a subject is determinedby the AP count, which indicates the number of vaccine antigens thatinduce T cell responses in a subject. The AP count of PolyPEPI1018 wasdetermined in each of the 433 subjects in the Model Population using thePEPI Test, and the AP50 count was then calculated for the ModelPopulation. The AP50 of PolyPEPI1018 in the Model Population is 4.73.The mean number of immunogenic antigens (i.e., antigens with ≥1 PEPI) inPolyPEPI1018 in a general population is 4.73. Abbreviations: AP=antigenswith ≥1 PEPI. Left Panel: Cumulative distribution curve. Right Panel:Distinct distribution curve.

FIGS. 25A-B—Effectiveness of PolyPEPI1018 CRC Vaccine in a generalpopulation. Vaccine induced T cells can recognize and kill tumor cellsif a PEPI in the vaccine is presented by the tumor cell. The number ofAGPs (expressed antigens with PEPI) is an indicator of vaccineeffectiveness in an individual, and is dependent on both the potency andantigenicity of PolyPEPI1018. The mean number of immunogenic CTAs (i.e.,AP [expressed antigens with ≥1 PEPI]) in PolyPEPI1018 is 2.54 in theModel Population. The likelihood that PolyPEPI1018 induces T cellresponses against multiple antigens in a subject (i.e., mAGP) in theModel Population is 77%.

DESCRIPTION OF THE SEQUENCES

SEQ ID NOs: 1 to 20 set forth 9 mer T cell epitopes described in Table30.

SEQ ID NOs: 21 to 40 set forth 9 mer T cell epitopes described in Table33.

SEQ ID NOs: 59, 60, 52, 53, 61, 63, 64, 65, 58 set forth the breastcancer vaccine peptides set forth in Table 31.

SEQ ID NOs 90, 81, 91, 92, 93, 84, 94, 86, 87 set forth the colorectalcancer vaccine peptides set forth in Table 34.

SEQ ID NOs: 103-115 set forth the additional peptide sequences describedin Table 17 and Table 19.

SEQ ID NOs: 116-128 set forth personalised vaccine peptides designed forpatient XYZ described in Table 26.

SEQ ID NOs: 129-140 set forth personalised vaccine peptides designed forpatient ABC described in Table 29.

SEQ ID NOs: 141-188 set forth further 9 mer T cell epitopes described inTable 41.

DETAILED DESCRIPTION

HLA Genotypes

HLAs are encoded by the most polymorphic genes of the human genome. Eachperson has a maternal and a paternal allele for the three HLA class Imolecules (HLA-A*, HLA-B*, HLA-C*) and four HLA class II molecules(HLA-DP*, HLA-DQ*, HLA-DRB1*, HLA-DRB3*/4*/5*).

Practically, each person expresses a different combination of 6 HLAclass I and 8 HLA class II molecules that present different epitopesfrom the same protein antigen. The function of HLA molecules is toregulate T cell responses. However up to date it was unknown how theHLAs of a person regulate T cell activation.

The nomenclature used to designate the amino acid sequence of the HLAmolecule is as follows: gene name*allele:protein number, which, forinstance, can look like: HLA-A*02:25. In this example, “02” refers tothe allele. In most instances, alleles are defined by serotypes—meaningthat the proteins of a given allele will not react with each other inserological assays. Protein numbers (“25” in the example above) areassigned consecutively as the protein is discovered. A new proteinnumber is assigned for any protein with a different amino acid sequence(e.g. even a one amino acid change in sequence is considered a differentprotein number). Further information on the nucleic acid sequence of agiven locus may be appended to the HLA nomenclature, but suchinformation is not required for the methods described herein.

The HLA class I genotype or HLA class II genotype of an individual mayrefer to the actual amino acid sequence of each class I or class II HLAof an individual, or may refer to the nomenclature, as described above,that designates, minimally, the allele and protein number of each HLAgene. An HLA genotype may be obtained or determined using any suitablemethod. For example, the sequence may be determined via sequencing theHLA gene loci using methods and protocols known in the art.Alternatively, the HLA set of an individual may be stored in a databaseand accessed using methods known in the art.

HLA-Epitope Binding

A given HLA of a subject will only present to T cells a limited numberof different peptides produced by the processing of protein antigens inan APC. As used herein, “display” or “present”, when used in relation toHLA, references the binding between a peptide (epitope) and an HLA. Inthis regard, to “display” or “present” a peptide is synonymous with“binding” a peptide.

As used herein, the term “epitope” or “T cell epitope” refers to asequence of contiguous amino acids contained within a protein antigenthat possess a binding affinity for (is capable of binding to) one ormore HLAs. An epitope is HLA- and antigen-specific (HLA-epitope pairs,predicted with known methods), but not subject specific. An epitope, a Tcell epitope, a polypeptide, a fragment of a polypeptide or acomposition comprising a polypeptide or a fragment thereof is“immunogenic” for a specific human subject if it is capable of inducinga T cell response (a cytotoxic T cell response or a helper T cellresponse) in that subject. In some cases the helper T cell response is aTh1-type helper T cell response. In some cases an epitope, a T cellepitope, a polypeptide, a fragment of a polypeptide or a compositioncomprising a polypeptide or a fragment thereof is “immunogenic” for aspecific human subject if it is more likely to induce a T cell responseor immune response in the subject than a different T cell epitope (or insome cases two different T cell epitopes each) capable of binding tojust one HLA molecule of the subject.

The terms “T cell response” and “immune response” are used hereininterchangeably, and refer to the activation of T cells and/or theinduction of one or more effector functions following recognition of oneor more HLA-epitope binding pairs. In some cases an “immune response”includes an antibody response, because HLA class II molecules stimulatehelper responses that are involved in inducing both long lasting CTLresponses and antibody responses. Effector functions includecytotoxicity, cytokine production and proliferation. According to thepresent disclosure, an epitope, a T cell epitope, or a fragment of apolypeptide is immunogenic for a specific subject if it is capable ofbinding to at least two, or in some cases at least three, class I or atleast two, or in some cases at least three or at least four class IIHLAs of the subject.

For the purposes of this disclosure we have coined the term “personalepitope”, or “PEPI” to distinguish subject specific epitopes from HLAspecific epitopes. A “PEPI” is a fragment of a polypeptide consisting ofa sequence of contiguous amino acids of the polypeptide that is a T cellepitope capable of binding to one or more HLA class I molecules of aspecific human subject. In other cases a “PEPI” is a fragment of apolypeptide consisting of a sequence of contiguous amino acids of thepolypeptide that is a T cell epitope capable of binding to one or moreHLA class II molecules of a specific human subject. In other words a“PEPI” is a T cell epitope that is recognised by the HLA set of aspecific individual. In contrast to an “epitope”, PEPIs are specific toan individual because different individuals have different HLA moleculeswhich each bind to different T cell epitopes.

“PEPI1” as used herein refers to a peptide, or a fragment of apolypeptide, that can bind to one HLA class I molecule (or, in specificcontexts, HLA class II molecule) of an individual. “PEPI1+” refers to apeptide, or a fragment of a polypeptide, that can bind to one or moreHLA class I molecule of an individual.

“PEPI2” refers to a peptide, or a fragment of a polypeptide, that canbind to two HLA class I (or II) molecules of an individual. “PEPI2+”refers to a peptide, or a fragment of a polypeptide, that can bind totwo or more HLA class I (or II) molecules of an individual, i.e. afragment identified according to a method of the disclosure.

“PEPI3” refers to a peptide, or a fragment of a polypeptide, that canbind to three HLA class I (or II) molecules of an individual. “PEPI3+”refers to a peptide, or a fragment of a polypeptide, that can bind tothree or more HLA class I (or II) molecules of an individual.

“PEPI4” refers to a peptide, or a fragment of a polypeptide, that canbind to four HLA class I (or II) molecules of an individual. “PEPI4+”refers to a peptide, or a fragment of a polypeptide, that can bind tofour or more HLA class I (or II) molecules of an individual.

“PEPI5” refers to a peptide, or a fragment of a polypeptide, that canbind to five HLA class I (or II) molecules of an individual. “PEPI5+”refers to a peptide, or a fragment of a polypeptide, that can bind tofive or more HLA class I (or II) molecules of an individual.

“PEPI6” refers to a peptide, or a fragment of a polypeptide, that canbind to all six HLA class I (or six HLA class II) molecules of anindividual.

Generally speaking, epitopes presented by HLA class I molecules areabout nine amino acids long and epitopes presented by HLA class IImolecules are about fifteen amino acids long. For the purposes of thisdisclosure, however, an epitope may be more or less than nine (for HLAClass I) or more or less than fifteen (for HLA Class II) amino acidslong, as long as the epitope is capable of binding HLA. For example, anepitope that is capable of binding to class I HLA may be between 7, or 8or 9 and 9 or 10 or 11 amino acids long. An epitope that is capable ofbinding to a class II HLA may be between 13, or 14 or 15 and 15 or 16 or17 amino acids long.

Therefore the disclosure herein includes, for example, a method ofpredicting whether a polypeptide is immunogenic for a relevantpopulation or cohort of human subjects (e.g., in a model humanpopulation) or identifying a fragment of a polypeptide as immunogenicfor a relevant population or cohort of human subjects (e.g., in a modelhuman population), the method comprising the steps of

-   -   (i) determining whether the polypeptide comprises:        -   a. a sequence of 7 to 11 consecutive amino acids that is            capable of binding to at least two HLA class I of the            subject; or        -   b. a sequence of 13 to 17 consecutive amino acids that is            capable of binding to at least two HLA class II of the            subject; and    -   (ii) predicting that the polypeptide is immunogenic for the        subject if the polypeptide comprises at least one sequence that        meets the requirements of step (i); or predicting that the        polypeptide is not immunogenic for the subject if the        polypeptide does not comprise at least one sequence that meets        the requirements of step (i); or identifying said consecutive        sequence of amino acids as the sequence of a fragment of the        polypeptide that is immunogenic for the subject.

Using techniques known in the art, it is possible to determine theepitopes that will bind to a known HLA. Any suitable method may be used,provided that the same method is used to determine multiple HLA-epitopebinding pairs that are directly compared. For example, biochemicalanalysis may be used. It is also possible to use lists of epitopes knownto be bound by a given HLA. It is also possible to use predictive ormodelling software to determine which epitopes may be bound by a givenHLA. Examples are provided in Table 1. In some cases a T cell epitope iscapable of binding to a given HLA if it has an IC50 or predicted IC50 ofless than 5000 nM, less than 2000 nM, less than 1000 nM, or less than500 nM.

TABLE 1 Example software for determining epitope-HLA binding WEB ADDRESSEPITOPE PREDICTION TOOLS BIMAS, NIHwww-bimas.cit.nih.gov/molbio/hla_bind/ PPAPROC, Tubingen Univ. MHCPred,Edward Jenner Inst. of Vaccine Res. EpiJen, Edward Jenner Inst. ofddg-pharmfac.net/epijen/EpiJen/EpiJen.htm Vaccine Res. NetMHC, Centerfor Biological cbs.dtu.dk/services/NetMHC/ Sequence Analysis SVMHC,Tubingen Univ. abi.inf.uni-tuebingen.de/Services/SVMHC/ SYFPEITHI,Biomedical Informatics,syfpeithi.de/bin/MHCServer.dll/EpitopePrediction.htm Heidelberg ETKEPITOOLKIT, Tubingen Univ. etk.informatik.uni-tuebingen.de/epipred/PREDEP, Hebrew Univ. Jerusalemmargalit.huji.ac.il/Teppred/mhc-bind/index.html RANKPEP, MIFBioinformatics bio.dfci.harvard.edu/RANKPEP/ IEDB, Immune EpitopeDatabase tools.immuneepitope.org/main/html/tcell_tools.html EPITOPEDATABASES MHCBN, Institute of Microbial imtech.res.in/raghava/mhcbn/Technology, Chandigarh, INDIA SYFPEITHI, Biomedical Informatics,syfpeithi.de/ Heidelberg AntiJen, Edward Jenner Inst. ofddg-pharmfac.net/antijen/AntiJen/antijenhomepage.htm Vaccine Res. EPIMHCdatabase of MHC ligands, immunax.dfci.harvard.edu/epimhc/ MIFBioinformatics IEDB, Immune Epitope Database iedb.org/

As provided herein T cell epitope presentation by multiple HLAs of anindividual is generally needed to trigger a T cell response.Accordingly, the methods of the disclosure comprise determining whethera polypeptide has a sequence that is a T cell epitope capable of bindingto at least two HLA class I molecules or at least two HLA class II(PEPI2+) molecules of a human subject (e.g., in a model humanpopulation).

The best predictor of a cytotoxic T cell response to a given polypeptideis the presence of at least one T cell epitope that is presented bythree or more HLA class I molecules of an individual (≥1 PEPI3+).Accordingly, in some cases the method comprises determining whether apolypeptide has a sequence that is a T cell epitope capable of bindingto at least three HLA class I molecules of a specific human subject. Insome cases the method comprises determining whether a polypeptide has asequence that is a T cell epitope capable of binding to just three HLAclass I of a human subject (e.g., in a model human population). A helperT cell response may be predicted by the presence of at least one T cellepitope that is presented by three or more (≥1 PEPI3+) or 4 or more (≥1PEPI4+) HLA class II of an individual. Therefore in some cases, themethod comprises determining whether a polypeptide has a sequence thatis a T cell epitope capable of binding to at least three HLA class II ofa human subject (e.g., in a model human population). In other cases, themethod comprises determining whether a polypeptide has a sequence thatis a T cell epitope capable of binding to at least four HLA class II ofa human subject. In other cases, the method comprises determiningwhether a polypeptide has a sequence that is a T cell epitope capable ofbinding to at just three and/or just four HLA class II of a humansubject.

In some cases, the disclosed methods and compositions may be used topredict whether a polypeptide/fragment will induce both a cytotoxic Tcell response and a helper T cell response in a human subject. Thepolypeptide/fragment comprises both an amino acid sequence that is a Tcell epitope capable of binding to multiple HLA class I molecules of thesubject and an amino acid sequence that is a T cell epitope capable ofbinding to multiple HLA class II molecules of the subject. The HLA classI-binding and HLA class II-binding epitopes may fully or partiallyoverlap. In some cases such fragments of a polypeptide may be identifiedby selecting an amino acid sequence that is a T cell epitope capable ofbinding to multiple (e.g. at least two or at least three) HLA class Imolecules of the subject, and then screening one or more longerfragments of the polypeptide that are extended at the N- and/orC-terminus for binding to one or more or the most possible (i.e. when nosuitable HLA class II-binding PEPI3+s are available) HLA class IImolecules of the subject or of a high percentage of subjects in apopulation.

Some subjects may have two HLA alleles that encode the same HLA molecule(for example, two copies for HLA-A*02:25 in case of homozygosity). TheHLA molecules encoded by these alleles bind all of the same T cellepitopes. For the purposes of this disclosure “binding to at least twoHLA molecules of the subject” as used herein includes binding to the HLAmolecules encoded by two identical HLA alleles in a single subject. Inother words, “binding to at least two HLA molecules of the subject” andthe like could otherwise be expressed as “binding to the HLA moleculesencoded by at least two HLA alleles of the subject”.

Polypeptide Antigens

As used herein, the term “polypeptide” refers to a full-length protein,a portion of a protein, or a peptide characterized as a string of aminoacids. As used herein, the term “peptide” refers to a short polypeptidecomprising between 2, or 3, or 4, or 5, or 6, or 7, or 8, or 9, or 10,or 11, or 12, or 13, or 14, or 15 and 10, or 11, or 12, or 13, or 14, or15, or 20, or 25, or 30, or 35, or 40, or 45, or 50 amino acids.

The terms “fragment” or “fragment of a polypeptide” as used herein referto a string of amino acids or an amino acid sequence typically ofreduced length relative to the or a reference polypeptide andcomprising, over the common portion, an amino acid sequence identical tothe reference polypeptide. Such a fragment according to the disclosuremay be, where appropriate, included in a larger polypeptide of which itis a constituent. In some cases the fragment may comprise the fulllength of the polypeptide, for example where the whole polypeptide, suchas a 9 amino acid peptide, is a single T cell epitope.

In some cases the polypeptide is, or the polypeptide consists of all orpart of an antigen that is, expressed by a pathogenic organism (forexample, a bacteria or a parasite), a virus, or a cancer cell, that isassociated with an autoimmune disorder or response or adisease-associated cell, or that is an allergen, or an ingredient of amedicine or pharmaceutical composition such as a vaccine orimmunotherapy composition. In some cases the method of the disclosurecomprises an initial step of identifying or selecting a suitablepolypeptide, for example a polypeptide as further described below.

The polypeptide or antigen may be expressed in the cells or specificallyin diseased cells of the specific or target human population (e.g. atumor-associated antigen, a polypeptide expressed by a virus,intracellular bacteria or parasite, or the in vivo product of a vaccineor immunotherapy composition) or acquired from the environment (e.g. afood, an allergen or a drug). The polypeptide or antigen may be presentin a sample taken from a subject of the specific or target humanpopulation. Both polypeptide antigens and HLAs can be exactly defined byamino acid or nucleotide sequences and sequenced using methods known inthe art.

The polypeptide or antigen may be a cancer- or tumor-associated antigen(TAA). TAAs are proteins expressed in cancer or tumor cells. The canceror tumour cell may be present in a sample obtained from a subject of thespecific or target human population. Examples of TAAs include newantigens (neoantigens) expressed during tumorigenesis, products ofoncogenes and tumor suppressor genes, overexpressed or aberrantlyexpressed cellular proteins (e.g. HER2, MUC1), antigens produced byoncogenic viruses (e.g. EBV, HPV, HCV, HBV, HTLV), cancer testisantigens (CTA)(e.g. MAGE family, NY-ESO) and cell-type-specificdifferentiation antigens (e.g. MART-1). TAA sequences may be foundexperimentally, or in published scientific papers, or through publiclyavailable databases, such as the database of the Ludwig Institute forCancer Research (cta.lncc.br/), Cancer Immunity database(cancerimmunity.org/peptide/) and the TANTIGEN Tumor T cell antigendatabase (cvc.dfci.harvard.edu/tadb/).

In some cases the polypeptide or antigen is not expressed or isminimally expressed in normal healthy cells or tissues, but is expressed(in those cells or tissues) in a high proportion of (with a highfrequency in) subjects having a particular disease or condition, such asa type of cancer or a cancer derived from a particular cell type ortissue, for example breast cancer, ovarian cancer or melanoma. A furtherexample is colorectal cancer. Other non-limiting cancer examples includenon-melanoma skin, lung, prostate, kidney, bladder, stomach, liver,cervix uteri, oesophagus, non-Hodgkin lymphoma, leukemia, pancreas,corpus uteri, lip, oral cavity, thyroid, brain, nervous system,gallbladder, larynx, pharynx, myeloma, nasopharynx, Hodgkin lymphoma,testis and Kaposi sarcoma. Alternatively, the polypeptide may beexpressed at low levels in normal healthy cells, but at high levels(overexpressed) in diseased (e.g. cancer) cells or in subjects havingthe disease or condition. In some cases the polypeptide is expressed in,or expressed at a high level relative to normal healthy cells orsubjects in, at least 2%, 5%, 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%,50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95% or more of suchindividuals, or of a subject-matched human subpopulation or model ortarget population. For example the population may be matched to thesubject by ethnicity, geographical location, gender, age, disease,disease type or stage, genotype, or expression of one or morebiomarkers.

In some cases the expression frequencies can be determined frompublished figures and scientific publications. In some cases the methodof the disclosure comprises a step of identifying or selecting such apolypeptide.

In some cases the polypeptide is associated with or highly (over-)expressed in cancer cells, or in solid tumors. Exemplary cancers includecarcinomas, sarcomas, lymphomas, leukemias, germ cell tumors, orblastomas. The cancer may or may not be a hormone related or dependentcancer (e.g., an estrogen or androgen related cancer). The tumor may bemalignant or benign. The cancer may or may not be metastatic.

In some cases the polypeptide is a cancer testis antigens (CTA). CTA arenot typically expressed beyond embryonic development in healthy cells.In healthy adults, CTA expression is limited to male germ cells that donot express HLAs and cannot present antigens to T cells. Therefore, CTAsare considered expressional neoantigens when expressed in cancer cells.

CTA expression is (i) specific for tumor cells, (ii) more frequent inmetastases than in primary tumors and (iii) conserved among metastasesof the same patient (Gajewski ed. Targeted Therapeutics in Melanoma.Springer New York. 2012).

The polypeptide may be a mutational neoantigen, which is expressed by acell, for example a cancer cell, of the individual, but altered from theanalogous protein in a normal or healthy cell. In some cases the methodsof the disclosure comprise the step of identifying a polypeptide that isa mutational neoantigen, or that is a mutational neoantigen in thespecific human subject, or of identifying a neoepitope. For example theneoantigen may be present in a sample obtained from the subject.Mutational neoantigens or neoepitopes can be used to targetdisease-associated cells, such as cancer cells, that express theneoantigen or a neoantigen comprising the neoepitope. Mutations in apolypeptide expressed by a cell, for example a cell in a sample takenfrom a subject, can be detected by, for example, sequencing, but themajority do not induce an immune response against theneoantigen-expressing cells. Currently, the identification of mutationalneoantigens that do induce an immune response is based on prediction ofmutational HLA restricted epitopes and further in vitro testing of theimmunogenicity of predicted epitopes in individual's blood specimen.This process is inaccurate, long and expensive.

The identification of mutational epitopes (e.g., neoepitopes) that bindto multiple HLA molecules reproducibly define the immunogenicity ofmutational neoantigens. Therefore, in some cases in accordance with thedisclosure, the polypeptide is a mutational neoantigen, and theimmunogenic fragment of the polypeptide comprises a neoantigen specificmutation (or consists of a neoepitope).

The polypeptide may be a viral protein that is expressedintracellularly. Examples include HPV16 E6, E7; HIV Tat, Rev, Gag, Pol,Env; HTLV-Tax, Rex, Gag, Env, Human herpes virus proteins, Dengue virusproteins. The polypeptide may be a parasite protein that is expressedintracellularly, for example malaria proteins.

The polypeptide may be an active ingredient of a pharmaceuticalcomposition, such as a vaccine or immunotherapy composition, optionallya candidate active ingredient for a new pharmaceutical composition. Theterm “active ingredient” as used herein refers to a polypeptide that isintended to induce an immune response and may include a polypeptideproduct of a vaccine or immunotherapy composition that is produced invivo after administration to a subject. For a DNA or RNA immunotherapycomposition, the polypeptide may be produced in vivo by the cells of asubject to whom the composition is administered. For a cell-basedcomposition, the polypeptide may be processed and/or presented by cellsof the composition, for example autologous dendritic cells or antigenpresenting cells pulsed with the polypeptide or comprising an expressionconstruct encoding the polypeptide. The pharmaceutical composition maycomprise a polynucleoide or cell encoding one or more active ingredientpolypeptides.

In other cases the polypeptide may be a target polypeptide antigen of apharmaceutical, vaccine or immunotherapy composition. A polypeptide is atarget polypeptide antigen if the composition is intended or designed toinduce an immune response (e.g. a cytotoxic T cell response) thattargets or is directed at the polypeptide. A target polypeptide antigenis typically a polypeptide that is expressed by a pathogenic organism, avirus or a diseased cell such as a cancer cell. A target polypeptideantigens may be a TAA or a CTA. Presently, >200 clinical trials areinvestigating cancer vaccines with tumor antigens.

The polypeptide may be an allergen that enters the body of an individualthrough, for example, the skin, lung or oral routes.

Non-limiting examples of suitable polypeptides include those listed inone or more of Tables 2 to 6.

Genetic sequences may be obtained from the sequencing of biologicalmaterials. Sequencing can be done by any suitable method that determinesDNA and/or RNA and/or amino acid sequences. The disclosure utilizes boththe HLA genotypes and amino acid sequences. However, methods to identifyHLA genotype from genetic sequences of an individual and methods ofobtaining amino acid sequences derived from DNA or RNA sequence data arenot the subject of the disclosure.

TABLE 2 LIST OF NAMED TUMOUR ANTIGENS WITH CORRESPONDING ACCESSIONNUMBERS. CTAs = bold and * 5T4 Q13641.1 A1BG P04217.1 A33 Q99795.1A4GALT Q9NPC4.1 AACT P01011.1 AAG Q9M6E9.1 ABI1 Q8IZP0.1 ABI2 Q9NYB9.1ABL1 P00519.1 ABL-BCR Q8WUG5.1 ABLIM3 O94929.1 ABLL P42684.1 ABTB1Q969K4.1 ACACA Q13085.1 ACBD4 Q8NC06.1 ACO1 P21399.1 ACRBP Q8NEB7.1*ACTL6A O96019.1 ACTL8 Q9H568.1* ACTN4 O43707.1 ACVR1 Q04771.1 ACVR1BP36896.1 ACVR2B Q13705.1 ACVRL1 P37023.1 ACS2B Q68CK6.1 ACSL5 Q9ULC5.1ADAM-15 Q13444.1 ADAM17 P78536.1 ADAM2 Q99965.1* ADAM29 Q9UKF5.1* ADAM7Q9H2U9.1 ADAP1 O75689.1 ADFP Q99541.1 ADGRA3 Q8IWK6.1 ADGRF1 Q5T601.1ADGRF2 Q8IZF7.1 ADGRL2 O95490.1 ADHFE1 Q8IWW8.1 AEN Q8WTP8.1 AFF1P51825.1 AFF4 Q9UHB7.1 AFP P02771.1 AGAP2 Q99490.1 AGO1 Q9UL18.1 AGO3Q9H9G7.1 AGO4 Q9HCK5.1 AGR2 O95994.1 AIFM2 Q9BRQ8.1 AIM2 O14862.1AKAP-13 Q12802.1 AKAP-3 O75969.1* AKAP-4 Q5JQC9.1* AKIP1 Q9NQ31.1 AKT1P31749.1 AKT2 P31751.1 AKT3 Q9Y243.1 ALDH1A1 P00352.1 ALK Q9UM73.1ALKBH1 Q13686.1 ALPK1 Q96QP1.1 AMIGO2 Q865J2.1 ANG2 O15123.1 ANKRD45Q5TZF3.1* ANO1 Q5XXA6.1 ANP32A P39687.1 ANXA2 P07355.1 APC P25054.1 APEHP13798.1 APOA2 P02652.1 APOD P05090.1 APOL1 O14791.1 AR P10275.1 ARAFP10398.1 ARF4L P49703.1 ARHGEF5 Q12774.1 ARID3A Q99856.1 ARID4A P29374.1ARL6IP5 O75915.1 ARMC3 B4DXS3.1* ARMC8 Q8IUR7.1 ARTC1 P52961.1 ARXQ96Q53.1* ATAD2 Q6PL18.1 ATIC P31939.1 AURKC Q9UQB9.1 AXIN1 O15169.1 AXLP30530.1 BAAT Q14032.1 BAFF Q9Y275.1 BAGE-1 Q13072.1* BAGE-2 Q86Y30.1*BAGE-3 Q86Y29.1* BAGE-4 Q86Y28.1 BAGE-5 Q86Y27.1* BAI1 O14514.1 BALP19835.1 BALF2 P03227.1 BALF4 P03188.1 BALF5 P03198.1 BARF1 P03228.1BBRF1 P03213.1 BCAN Q96GW7.1 BCAP31 P51572.1 BCL-2 P10415.1 BCL2L1Q07817.1 BCL6 P41182.1 BCL9 O00512.1 BCR P11274.1 BCRF1 P03180.1 BDLF3P03224.1 BGLF4 P13288.1 BHLF1 P03181.1 BHRF1 P03182.1 BILF1 P03208.1BILF2 P03218.1 BIN1 O00499.1 BING-4 O15213.1 BIRC7 Q96CA5.1 BLLF1P03200.1 BLLF2 P03199.1 BMI1 P35226.1 BMLF1 Q04360.1 BMPR1B O00238.1BMRF1 P03191.1 BNLF2a P00739.1 BNLF2b Q8AZJ3.1 BNRF1 P03179.1 BRAF1P15056.1 BRD4 O60885.1 BRDT Q58F21.1* BRI3BP Q8WY22.1 BRINP1 O60477.1BRLF1 P03209.1 BTBD2 Q9BX70.1 BUB1B O60566.1 BVRF2 P03234.1 BXLF1P03177.1 BZLF1 P03206.1 C15orf60 Q7Z4M0.1* CA 12-5 Q8WXI7.1 CA 19-9Q969X2.1 CA195 Q5TG92.1 CA9 Q16790.1 CABYR O75952.1* CADM4 Q8NFZ8.1CAGE1 Q8CT20.1* CALCA P01258.1 CALR3 Q96L12.1 CAN P35658.1 CASC3O15234.1 CASC5 Q8NG31.1* CASP5 P51878.1 CASP8 Q14790.1 CBFA2T2 O43439.1CBFA2T3 O75081.1 CBL P22681.1 CBLB Q13191.1 CC3 Q9BUP3.1 CCDC110Q8TBZ0.1* CCDC33 Q8N5R6.1* CCDC36 Q8IYA8.1* CCDC6 Q16204.1 CCDC62Q6P9F0.1* CCDC68 Q9H2F9.1 CCDC83 Q8IWF9.1* CCL13 Q99616.1 CCL2 P13500.1CCL7 P80098.1 CCNA1 P78396.1* CCNA2 P20248.1 CCNB1 P14635.1 CCND1P24385.1 CCNE2 096020.1 CCNI Q14094.1 CCNL1 Q9UK58.1 CCR2 P41597.1 CD105P17813.1 CD123 P26951.1 CD13 P15144.1 CD133 O43490.1 CD137 Q07011.1CD138 P18827.1 CD157 Q10588.1 CD16A P08637.1 CD178 P48023.1 CD19P15391.1 CD194 P51679.1 CD2 P06729.1 CD20 P11836.1 CD21 P20023.1 CD22P20273.1 CD229 Q9HBG7.1 CD23 P06734.1 CD27 P26842.1 CD28 P10747.1 CD30P28908.1 CD317 Q10589.1 CD33 P20138.1 CD350 Q9ULW2.1 CD36 P16671.1 CD37P11049.1 CD4 P01730.1 CD40 P25942.1 CD40L P29965.1 CD45 P08575.1 CD47Q08722.1 CD51 P06756.1 CD52 P31358.1 CD55 P08174.1 CD61 P05106.1 CD70P32970.1 CD74 P08922.1 CD75 P15907.1 CD79B P40259.1 CD80 P33681.1 CD86P42081.1 CD8a P01732.1 CD8b P10966.1 CD95 P25445.1 CD98 P08195.1 CDC123O75794.1 CDC2 P06493.1 CDC27 P30260.1 CDC73 Q6P1J9.1 CDCA1 Q9BZD4.1*CDCP1 Q9H5V8.1 CDH3 P22223.1 CDK2AP1 O14519.1 CDK4 P11802.1 CDK7P50613.1 CDKN1A P38936.1 CDKN2A P42771.1 CEA P06731.1 CEACAM1 Q86UE4.1CENPK Q9BS16.1 CEP162 Q5TB80.1 CEP290 O15078.1* CEP55 Q53EZ4.1* CFL1P23528.1 CH3L2 Q15782.1 CHEK1 O14757.1 CK2 P19784.1 CLCA2 Q9UQC9.1 CLOCKO15516.1 CLPP Q16740.1 CMC4 P56277.1 CML66 Q96RS6.1 CO-029 P19075.1COTL1 Q14019.1 COX2 P35354.1 COX6B2 Q6YFQ2.1* CPSF1 Q10570.1 CPXCR1Q8N123.1* CREBL2 O60519.1 CREG1 O75629.1 Cripto P13385.1 CRISP2P16562.1* *CRK P46108.1 CRKL P46109.1 CRLF2 Q9HC73.1 CSAGE Q6PB30.1 CT45Q5HYN5.1* CT45A2 Q5DJT8.1* CT45A3 Q8NHU0.1* CT45A4 Q8N7B7.1* CT45A5Q6NSH3.1* CT45A6 P0DMU7.1* CT46 Q86X24.1* CT47 Q5JQC4.1* CT47B1P0C2P7.1* CTAGE2 Q96RT6.1* cTAGE5 O15320.1* CTCFL Q8NI51.1* CTDSP2O14595.1 CTGF P29279.1 CTLA4 P16410.1 CTNNA2 P26232.1* CTNNB1 P35222.1CTNND1 O60716.1 CTSH P09668.1 CTSP1 A0RZH4.1* CTTN Q14247.1 CXCR4P61073.1 CXorf48 Q8WUE5.1* CXorf61 Q5H943.1* Cyclin-E P24864.1 CYP1B1Q16678.1 CypB P23284.1 CYR61 O00622.1 CS1 P28290.1 CSAG1 Q6PB30.1* CSDE1O75534.1 CSF1 P09603.1 CSF1R P07333.1 CSF3R Q99062.1 CSK P41240.1 CSK23Q8NEV1.1 DAPK3 O43293.1 DAZ1 Q9NQZ3.1 DBPC Q9Y2T7.1 DCAF12 Q5T6F0.1* DCTP40126.1 DCUN1D1 Q96GG9.1 DCUN1D3 Q8IWE4.1 DDR1 Q08345.1 DDX3X O00571.1DDX6 P26196.1 DEDD O75618.1 DEK P35659.1 DENR O43583.1 DEPDC1 Q5TB30.1DFNA5 O60443.1 DGAT2 Q96PD7.1 DHFR P00374.1 DKK1 O94907.1 DKK3 Q9UBP4.1DKKL1 Q9UK85.1* DLEU1 O43261.1 DMBT1 Q9UGM3.1 DMRT1 Q9Y5R6.1* DNAJB8Q8NHS0.1* DNAJC8 O75937.1 DNMT3A Q9Y6K1.1 DPPA2 Q7Z7J5.1* DR4 O00220.1DR5 O14763.1 DRG1 Q9Y295.1* DSCR8 Q96T75.1 E2F3 O00716.1 E2F6 O75461.1E2F8 A0AVK6.1 EBNA1 P03211.1 EBNA2 P12978.1 EBNA3 P12977.1 EBNA4P03203.1 EBNA6 P03204.1 EBNA-LP Q8AZK7.1 E-cadherin P12830.1 ECT2Q9H8V3.1 ECTL2 Q00858.1 EDAG Q9BXL5.1* EEF2 P13639.1 EFNA1 P20827.1 EFSO43281.1 EFTUD2 Q15029.1 EGFL7 Q9UHF1.1 EGFR p00533.1 E124 O14681.1EIF4EBP1 Q13541.1 ELF3 P78545.1 ELF4 Q99607.1 ELOVL4 Q9GZR5.1* EMP1P54849.1 ENAH Q8N8S7.1 Endosialin Q9HCU0.1 ENO1 P06733.1 ENO2 P09104.1ENO3 P13929.1 ENTPD5 O75356.1 EpCAM P16422.1 EPHA2 P29317.1 EPHA3P29320.1 EPHB2 P29323.1 EPHB4 P54760.1 EPHB6 O15197.1 EPS8 Q12929.1ERBB3 P21860.1 ERBB4 Q15303.1 EREG O14944.1 ERG P11308.1 ERVK-18O42043.1 ERVK-19 O71037.1 ESR1 P03372.1 ETAA1 Q9NY74.1 ETS1 P14921.1ETS2 P15036.1 ETV1 P50549.1 ETV5 P41161.1 ETV6 P41212.1 EVI5 O60447.1EWSR1 Q01844.1 EYA2 O00167.1 EZH2 Q15910.1 FABP7 O15540.1 FAM133AQ8N9E0.1* FAM13A O94988.1 FAM46D Q8NEK8.1* FAM58BP P0C7Q3.1 FANCGO15287.1 FATE1 Q969F0.1* FBXO39 Q8N4B4.1* FBXW11 Q9UKB1.1 FCHSD2O94868.1 FER P16591.1 FES P07332.1 FEV Q99581.1 FGF10 O15520.1 FGF23Q9GZV9.1 FGF3 P11487.1 FGF4 P08620.1 FGF5 P12034.1 FGFR1 P11362.1 FGFR2P21802.1 FGFR3 P22607.1 FGFR4 P22455.1 FGR P09769.1 FLI1 Q01543.1 FLT3P36888.1 FMNL1 O95466.1 FMOD Q06828.1 FMR1NB Q8N0W7.1* FN1 P02751.1 Fn14Q9NP84.1 FNIP2 Q9P278.1 FOLR1 P15328.1 FOS P01100.1 FosB P53539.1 FOSL1P15407.1 FOXM1 Q08050.1 FOXO1 Q12778.1 FOXO3 O43524.1 FRAT1 Q92837.1FRMD3 A2A2Y4.1 FSIP1 Q8NA03.1 FSIP2 Q5CZCO.1 FSTL3 O95633.1 FTHL17Q9BXU8.1* FUNDC2 Q9BWH2.1 FUS P35637.1 FUT1 P19526.1 FUT3 P21217.1 FYNP06241.1 GAB2 Q9UQC2.1 GADD45G O95257.1 GAGE-1 Q13065.1 GAGE12B/C/D/EA1L429.1 GAGE12F P0CL80.1 GAGE12G P0CL81.1 GAGE12H A6NDE8.1 GAGE12IP0CL82.1 GAGE12J A6NER3.1 GAGE-2 Q6NT46.1 GAGE-3 Q13067.1 GAGE-4Q13068.1 GAGE-5 Q13069.1 GAGE-6 Q13070.1 GAGE-7 O76087.1 GAGE-8 Q9UEU5.1GALGT2 Q00973.1 GAS7 O60861.1 GASZ Q8WWH4.1 GATA-3 P23771.1 GBU4-5Q587J7.1 GCDFP-15 P12273.1 GFAP P14136.1 GFI1 Q99684.1 Ghrelin Q9UBU3.1GHSR Q92847.1 GIPC1 O14908.1 GITR Q9Y5U5.1 GKAP1 Q5VSY0.1 GLI1 P08151.1Glypican-3 P51654.1 GML Q99445.1 GNA11 P29992.1 GNAQ P50148.1 GNB2L1P63244.1 GOLGA5 Q8TBA6.1 gp100 P40967.1 gp75 P17643.1 Gp96 P14625.1GPAT2 Q6NUI2.1* GPATCH2 Q9NW75.1* GPC-3 P51654.1 GPNMB Q14956.1 GPR143P51810.1 GPR89A B7ZAQ6.1 GRB2 P62993.1 GRP78 P11021.1 GUCY1A3 Q02108.1H3F3A P84243.1 HAGE Q9NXZ2.1* hANP P01160.1 HBEGF Q99075.1 hCG-betaP01233.1 HDAC1 Q13547.1 HDAC2 Q92769.1 HDAC3 O15379.1 HDAC4 P56524.1HDAC5 Q9UQL6.1 HDAC6 Q9UBN7.1 HDAC7 Q8WUI4.1 HDAC8 Q9BY41.1 HDAC9Q9UKV0.1 HEATR1 Q9H583.1 Hepsin P05981.1 Her2/neu P04626.1 HERC2O95714.1 HERV-K104 P61576.1 HEXB P07686.1 HEXIM1 O94992.1 HGRG8 Q9Y5A9.1HIPK2 Q9H2X6.1 HJURP Q8NCD3.1 HMGB1 P09429.1 HMOX1 P09601.1 HNRPLP14866.1 HOM-TES-85 Q9P127.1* HORMAD1 Q86X24.1* HORMAD2 Q8N7B1.1* HPSEQ9Y251.1 HPV16 E6 P03126.1 HPV16 E7 P03129.1 HPV18 E6 P06463.1 HPV18 E7P06788.1 HRAS P01112.1 HSD17B13 Q7Z5P4.1 HSP105 Q92598.1 HSP60 P10809.1HSPA1A P08107.1 HSPB9 Q9BQS6.1* HST-2 P10767.1 HT001 Q2TB18.1 hTERTO14746.1 HUS1 O60921.1 ICAM-1 P05362.1 IDH1 O75874.1 IDO1 P14902.1 IER3P46695.1 IGF1R P08069.1 IGFS11 Q5DX21.1* IL13RA2 Q14627.1* IMP-3Q9NV31.1* ING3 Q9NXR8.1 INPPL1 O15357.1 INTS6 Q9UL03.1 IRF4 Q15306.1IRS4 O14654.1 ITGA5 P08648.1 ITGB8 P26012.1 ITPA Q9BY32.1 ITPR2 Q14571.1JAK2 O60674.1 JAK3 P52333.1 JARID1B Q9UGL1.1* JAZF1 Q86VZ6.1 JNK1P45983.1 JNK2 P45984.1 JNK3 P53779.1 JTB O76095.1 JUN P05412.1 JUPP14923.1 K19 P08727.1 KAAG1 Q9UBP8.1 Kallikrein 14 Q9P0G3.1 Kallikrein 4Q9Y5K2.1 KAT6A Q92794.1 KDM1A O60341.1 KDM5A P29375.1 KIAA0100 Q14667.1*KIAA0336 Q8IWJ2.1 KIAA1199 Q8WUJ3.1 KIAA1641 A6QL64.1 KIF11 P52732.1KIF1B O60333.1 KIF20A O95235.1 KIT P10721.1 KLF4 O43474.1 KLHL41O60662.1 KLK10 O43240.1 KMT2D O14686.1 KOC1 O00425.1 K-ras P01116.1KRIT1 O00522.1 KW-12 P62913.1 KW-2 Q96RS0.1 KW-5 (SEBD4) Q9HOZ9.1 KW-7O75475.1 L1CAM P32004.1 L53 Q96EL3.1 L6 Q9BTT4.1 LAG3 P18627.1 Lage-1O75638.1* LATS1 O95835.1 LATS2 Q9NRM7.1 LCMT2 O60294.1 LCP1 P13796.1LDHC P07864.1* LDLR P01130.1 LEMD1 Q68G75.1* Lengsin Q5TDP6.1 LETMD1Q6P1Q0.1 LGALS3BP Q08380.1 LGALS8 O00214.1 LIN7A O14910.1 LIPI Q6XZB0.1*LIV-1 Q13433.1 LLGL1 Q15334.1 LMO1 P25800.1 LMO2 P25791.1 LMP1 P03230.1LMP2 P13285.1 LOC647107 Q8TAI5.1* LOXL2 Q9Y4K0.1 LRP1 Q07954.1 LRRN2O75325.1 LTF P02788.1 LTK P29376.1 LZTS1 Q9Y250.1 LY6K Q17RY6.1* LYNP07948.1 LYPD6B Q8NI32.1* MAEA Q7L5Y9.1 MAEL Q96JY0.1* MAF O75444.1 MAFFQ9ULX9.1 MAFG O15525.1 MAFK O60675.1 MAGE-A1 P43355.1* MAGE-A10P43363.1* MAGE-A11 P43364.1* MAGE-A12 P43365.1* MAGE-A2 P43356.1*MAGE-A2B Q6P448.1* MAGE-A3 P43357.1* MAGE-A4 P43358.1* MAGE-A5 P43359.1*MAGE-A6 P43360.1* MAGE-A8 P43361.1* MAGE-A9 P43362.1* MAGE-B1 P43366.1*MAGE-B2 O15479.1* MAGE-B3 O15480.1* MAGE-B4 O15481.1* MAGE-B5 Q9BZ81.1*MAGE-B6 Q8N7X4.1* MAGE-C1 O60732.1* MAGE-C2 Q9UBF1.1* MAGE-C3 Q8TD91.1*mammaglobin-A Q13296.1 MANF P55145.1 MAP2K2 P36507.1 MAP2K7 O14733.1MAP3K7 O43318.1 MAP4K5 Q9Y4K4.1 MART1 Q16655.1 MART-2 Q5VTY9.1 MAS1P04201.1 MC1R Q01726.1 MCAK Q99661.1* MCF2 P10911.1 MCF2L O15068.1 MCL1Q07820.1 MCTS1 Q9ULC4.1 MCSP Q6UVK1.1 MDK P21741.1 MDM2 Q00987.1 MDM4O15151.1 ME1 P48163.1 ME491 P08962.1 MECOM Q03112.1 MELK Q14680.1 MEN1O00255.1 MERTK Q12866.1 MET P08581.1 MFGE8 Q08431.1 MFHAS1 Q9Y4C4.1 MFI2P08582.1 MGAT5 Q09328.1 Midkine P21741.1 MIF P14174.1 MKI67 P46013.1MLH1 P40692.1 MLL Q03164.1 MLLT1 Q03111.1 MLLT10 P55197.1 MLLT11Q13015.1 MLLT3 P42568.1 MLLT4 P55196.1 MLLT6 P55198.1 MMP14 P50281.1MMP2 P08253.1 MMP7 P09237.1 MMP9 P14780.1 MOB3B Q86TA1.1 MORC1 Q86VD1.1*MPHOSPH1 Q96Q89.1* MPL P40238.1 MRAS O14807.1 MRP1 P33527.1 MRP3O15438.1 MRPL28 Q13084.1 MRPL30 Q8TCC3.1 MRPS11 P82912.1 MSLN Q13421.1MTA1 Q13330.1 MTA2 O94776.1 MTA3 Q9BTC8.1 MTCP1 P56278.1 MTSS1 O43312.1MUC-1 P15941.1 MUC-2 Q02817.1 MUC-3 Q02505.1 MUC-4 Q99102.1 MUC-5ACP98088.1 MUC-6 Q6W4X9.1 MUM1 Q2TAK8.1 MUM2 Q9Y5R8.1 MYB P10242.1 MYCP01106.1 MYCL P12524.1 MYCLP1 P12525.1 MYCN P04198.1 MYD88 Q99836.1MYEOV Q96EZ4.1 MYO1B O43795.1 NA88-A P0C5K6.1* NAE1 Q13564.1 Napsin-AO96009.1 NAT6 Q93015.1 NBAS A2RRP1.1 NBPF12 Q5TAG4.1 NCOA4 Q13772.1NDC80 O14777.1 NDUFC2 O95298.1 Nectin-4 Q96NY8.1 NEK2 P51955.1 NEMFO60524.1 NENF Q9UMX5.1 NEURL1 O76050.1 NFIB O00712.1 NFKB2 Q00653.1NF-X1 Q12986.1 NFYC Q13952.1 NGAL P80188.1 NGEP Q6IWH7.1 NKG2D-L1Q9BZM6.1 NKG2D-L2 Q9BZM5.1 NKG2D-L3 Q9BZM4.1 NKG2D-L4 Q8TD07.1 NKX3.1Q99801.1 NLGN4X Q8N0W4.1 NLRP4 Q96MN2.1* NNMT P40261.1 NOL4 O94818.1*NOTCH2 Q04721.1 NOTCH3 Q9UM47.1 NOTCH4 Q99466.1 NOV P48745.1 NPM1P06748.1 NR6A1 Q15406.1* N-RAS P01111.1 NRCAM Q92823.1 NRP1 O14786.1NSE1 Q96KN4.1 NSE2 Q96KN1.1 NTRK1 P04629.1 NUAK1 O60285.1 NUGGC Q68CJ6.1NXF2 Q9GZY0.1* NXF2B Q5JRM6.1* NY-BR-1 Q9BXX3.1 NYD-TSPG Q9BWV7.1NY-ESO-1 P78358.1* NY-MEL-1 P57729.1 OCA2 Q04671.1 ODF1 Q14990.1* ODF2Q5BJF6.1* ODF3 Q96PU9.1* ODF4 Q2M2E3.1* OGG1 O15527.1 OCT O15294.1 OIP5O43482.1* OS9 Q13438.1 OTOA Q05BM7.1* OX40 P43489.1 OX4OL P23510.1 P53P04637.1 P56-LCK P06239.1 PA2G4 Q9UQ80.1 PAGE1 O75459.1* PAGE2 Q7Z2X2.1*PAGE2B Q5JRK9.1* PAGE3 Q5JUK9.1* PAGE4 O60829.1* PAGE5 Q96GU1.1* PAK2Q13177.1 PANO1 I0J062.1 PAP Q06141.1 PAPOLG Q9BWT3.1 PARK2 O60260.1PARK7 Q99497.1 PARP12 Q9H0J9.1 PASD1 Q8IV76.1* PAX3 P23760.1 PAX5Q02548.1 PBF P00751.1 PBK Q96KB5.1* PBX1 P40424.1 PCDC1 Q15116.1 PCM1Q15154.1 PCNXL2 A6NKB5.1 PDGFB P01127.1 PDGFRA P16234.1 PEPP2 Q9HAU0.1*PGF P49763.1 PGK1 P00558.1 PHLDA3 Q9Y5J5.1 PHLPP1 O60346.1 PIAS1O75925.1 PIAS2 O75928.1 PIK3CA P42336.1 PIK3CD O00329.1 PIK3R2 O00459.1PIM1 P11309.1 PIM2 Q9P1W9.1 PIM3 Q86V86.1 PIR O00625.1 PIWIL1 Q96J94.1*PIWIL2 Q8TC59.1* PIWIL3 Q7Z3Z3.1 PIWIL4 Q7Z3Z4.1 PKN3 Q6P5Z2.1 PLA2G16P53816.1 PLAC1 Q9HBJ0.1* PLAG1 Q6DJT9.1 PLEKHG5 O94827.1 PLK3 Q9H4B4.1PLS3 P13797.1 PLVAP Q9BX97.1 PLXNB1 O43157.1 PLXNB2 O15031.1 PMLP29590.1 PML-RARA Q96QH2.1 POTEA Q6S8J7.1* POTEB Q6S5H4.1* POTECB2RU33.1* POTED Q86YR6.1* POTEE Q6S8J3.1* POTEG Q6S5H5.1* POTEHQ6S545.1* PP2A P63151.1 PPAPDC1B Q8NEB5.1 PPFIA1 Q13136.1 PPIG Q13427.1PPP2R1B P30154.1 PRAME P78395.1* PRDX5 P30044.1 PRKAA1 Q13131.1 PRKCIP41743.1 PRM1 P04553.1* PRM2 P04554.1* PRMT3 O60678.1 PRMT6 Q96LA8.1PDL1 Q9NZQ7.1 PROM1 O43490.1 PRSS54 Q6PEW0.1* PRSS55 Q6UWB4.1* PRTN3P24158.1 PRUNE Q86TP1.1 PRUNE2 Q8WUY3.1 PSA P07288.1 PSCA D3DWI6.1 PSMAQ04609.1 PSMD10 O75832.1 PSGR Q9H255.1 PSP-94 Q1L6U9.1 PTEN P60484.1PTH-rP P12272.1 PTK6 Q13882.1 PTPN20A Q4JDL3.1* PTPRK Q15262.1 PTPRZP23471.1 PTTG-1 O95997.1 PTTG2 Q9NZH5.1 PTTG3 Q9NZH4.1 PXDNL A1KZ92.1RAB11FIP3 O75154.1 RAB8A P61006.1 RAD1 O60671.1 RAD17 O75943.1 RAD51CO43502.1 RAF1 P04049.1 RAGE-1 Q9UQ07.1 RAP1A P62834.1 RARA P10276.1RASSF10 A6NK89.1 RB1 P06400.1 RBL2 Q08999.1 RBM46 Q8TBY0.1* RBP4P02753.1 RCAS1 O00559.1 RCVRN P35243.1 RECQL4 O94761.1 RET P07949.1RGS22 Q8NE09.1* RGS5 O15539.1 RHAMM O75330.1 RhoC P08134.1 RHOXF2Q9BQY4.1 RL31 P62888.1 RNASET2 O00584.1 RNF43 Q68DV7.1 RNF8 O76064.1 RONQ04912.1 ROPN1A Q9HAT0.1* ROR1 Q01973.1 RPA1 O95602.1 RPL10A P62906.1RPL7A P62424.1 RPS2 P15880.1 RPS6KA5 O75582.1 RPSA P08865.1 RQCD1Q92600.1* RRAS2 P62070.1 RSL1D1 O76021.1 RTKN Q9BST9.1 RUNX1 Q01196.1RUNX2 Q13950.1 RYK P34925.1 SAGE1 Q9NXZ1.1* SART2 Q9UL01.1 SART3Q15020.1 SASH1 O94885.1 sCLU P10909.1 SCRN1 Q12765.1 SDCBP O00560.1SDF-1 P48061.1 SDHD O14521.1 SEC31A O94979.1 SEC63 Q9UGP8.1 Semaphorin4D Q92854.1 SEMG1 P04279.1* SFN P31947.1 SH2B2 O14492.1 SH2D1B O14796.1SH3BP1 Q9Y3L3.1 SHB Q15464.1 SHC3 Q92529.1 SIRT2 Q8IXJ6.1 SIVA1 O15304.1SKI P12755.1 SLBP A9UHW6.1 SLC22A10 Q63ZE4.1 SLC25A47 Q6Q0C1.1 SLC35A4Q96G79.1 SLC45A3 Q96JT2.1 SLC4A1AP Q9BWU0.1 SLCO6A1 Q86UG4.1* SLITRK6Q9H5Y7.1 Sm23 P27701.1 SMAD5 Q99717.1 SMAD6 O43541.1 SMO Q99835.1 Smt3BP61956.1 SNRPD1 P62314.1 SOS1 Q07889.1 SOX-2 P48431.1 SOX-6 P35712.1SOX-11 P35716.1 SPA17 Q15506.1* SPACA3 Q8IXA5.1* SPAG1 Q07617.1* SPAG17Q6Q759.1* SPAG4 Q9NPE6.1* SPAG6 O75602.1* SPAG8 Q99932.1* SPAG9O60271.1* SPANXA1 Q9NS26.1* SPANXB Q9N525.1* SPANXC Q9NY87.1* SPANXDQ9BXN6.1* SPANXE Q8TAD1.1* SPANXN1 Q5VSR9.1* SPANXN2 Q5MJ10.1* SPANXN3Q5MJ09.1* SPANXN4 Q5MJ08.1* SPANXN5 Q5MJ07.1* SPATA19 Q7Z5L4.1* SPEF2Q9C093.1* SPI1 P17947.1 SPINLW1 O95925.1* SPO11 Q9Y5K1.1* SRC P12931.1SSPN Q14714.1 SSX-1 Q16384.1* SSX-2 Q16385.1* SSX-3 Q99909.1* SSX-4O60224.1* SSX-5 O60225.1* SSX-6 Q7RTT6.1* SSX-7 Q7RTT5.1* SSX-9Q7RTT3.1* ST18 O60284.1 STAT1 P42224.1 STEAP1 Q9UHE8.1 STK11 Q15831.1STK25 O00506.1 STK3 Q13188.1 STN Q9H668.1 SUPT7L O94864.1 SurvivinO15392.1 SUV39H1 O43463.1 SYCE1 Q8N0S2.1 SYCP1 Q15431.1 SYCP3 Q8IZU3.1SYT Q15532.1 TA-4 Q96RI8.1 TACC1 O75410.1 TAF1B Q53T94.1 TAF4 O00268.1TAF7L Q5H9L4.1* TAG-1 Q02246.1* TALI P17542.1 TAL2 Q16559.1 TAPBPO15533.1 TATI P00995.1 TAX1BP3 O14907.1 TBC1D3 Q8IZP1.1 TBP-1 P17980.1TCL1A P56279.1 TCL1B O95988.1 TDHP Q9BT92.1 TDRD1 Q9BXT4.1* TDRD4Q9BXT8.1* TDRD6 O60522.1* TEXT5 Q96M29.1* TEX101 Q9BY14.1* TEX14Q8IWB6.1* TEX15 Q9BXT5.1* TEX38 Q6PEX7.1* TF P02787.1 TFDP3 Q5H910.1*TFE3 P19532.1 TGFBR1 P36897.1 TGFBR2 P37173.1 THEG Q9P2T0.1* TIE2Q02763.1 TIPRL O75663.1 TLR2 O60603.1 TMEFF1 Q8IYR6.1* TMEFF2 Q9UIK5.1*TMEM108 Q6UXF1.1* TMEM127 O75204.1 TMPRSS12 Q86W55.1* TNC P24821.1TNFRSF17 Q02223.1 TNFSF15 O95150.1 TNK2 Q07912.1 TOMM34 Q15785.1 TOP2AP11388.1 TOP2B Q02880.1 TOR3A Q9H497.1 TP73 O15350.1 TPA1 8N543.1 TPGS2Q68CL5.1 TPI1 P60174.1 TPL2 P41279.1 TPM4 P67936.1 TPO P40225.1 TPPP2P59282.1* TPR P12270.1 TPTE P56180.1* TRAF5 O00463.1 TRAG-3 Q9Y5P2.1*TRGC2 P03986.1 TRIM24 O15164.1 TRIM37 O94972.1 TRIM68 Q6AZZ1.1 TRPM8Q7Z2W7.1 TSGA10 Q9BZW7.1* TSP50 Q9UI38.1* TSPAN6 O43657.1 TSPY1Q01534.1* TSPY2 A6NKD2.1* TSPY3 Q6B019.1* TSPYL1 Q9H0U9.1 TSSK6Q9BXA6.1* TTC23 Q5W5X9.1 TTK P33981.1* TULP2 O00295.1* TUSC2 O75896.1TWEAK O43508.1 TXNIP Q9H3M7.1 TYMS P04818.1 TYR P14679.1 U2 snRNP BP08579.1 U2AF1 Q01081.1 UBD O15205.1 UBE2A P49459.1 UBE2C O00762.1UBE2V1 Q13404.1 UBE4B O95155.1 UBR5 O95071.1 UBXD5 Q5T124.1 UFL1O94874.1 URI1 O94763.1 URLC10 Q17RY6.1 UR0C1 Q96N76.1 USP2 O75604.1 USP4Q13107.1 VAV1 P15498.1 VCX3A Q9NNX9.1 VEGFR1 P17948.1 VEGFR2 P35968.1VHL P40337.1 VIM P08670.1 VWA5A O00534.1 WHSC2 Q9H3P2.1 WISP1 O95388.1WNK2 Q9Y351.1 WNT10B O00744.1 WNT3 P56703.1 WNT-5a P41221.1 WT1 P19544.1WWP1 Q9H0M0.1 XAGE-1 Q9HD64.1* XAGE-2 Q96GT9.1* XAGE-3 Q8WTP9.1* XAGE-4Q8WWM0.1 XAGE-5 Q8WWM1.1* XBP1 P17861.1 XPO1 O14980.1 XRCC3 O43542.1YB-1 P67809.1 YEATS4 O95619.1 YES1 P07947.1 YKL-40 P36222.1 ZBTB7AO95365.1 ZBTB7C A1YPR0.1 ZEB1 P37275.1 ZFYVE19 Q96K21.1 ZNF165 P49910.1*ZNF185 O15231.1 ZNF217 O75362.1 ZNF320 A2RRD8.1 ZNF395 Q9H8N7.1 ZNF645Q8N7E2.1* ZUBR1 Q5T4S7.1 ZW10 O43264.1 ZWINT O95229.1 5T4 Q13641.1 A1BGP04217.1 A33 Q99795.1 A4GALT Q9NPC4.1 AACT P01011.1 AAG Q9M6E9.1 ABI1Q8IZP0.1 ABI2 Q9NYB9.1 ABL1 P00519.1 ABL-BCR Q8WUG5.1 ABLIM3 O94929.1ABLL P42684.1 ABTB1 Q969K4.1 ACACA Q13085.1 ACBD4 Q8NC06.1 ACO1 P21399.1ACRBP Q8NEB7.1 ACTL6A O96019.1 ACTL8 Q9H568.1 ACTN4 O43707.1 ACVR1Q04771.1 ACVR1B P36896.1 ACVR2B Q13705.1 ACVRL1 P37023.1 ACS2B Q68CK6.1ACSL5 Q9ULC5.1 ADAM-15 Q13444.1 ADAM17 P78536.1 ADAM2 Q99965.1 ADAM29Q9UKF5.1 ADAM7 Q9H2U9.1 ADAP1 O75689.1 ADFP Q99541.1 ADGRA3 Q8IWK6.1ADGRF1 Q5T601.1 ADGRF2 Q8IZF7.1 ADGRL2 O95490.1 ADHFE1 Q8IWW8.1 AENQ8WTP8.1 AFF1 P51825.1 AFF4 Q9UHB7.1 AFP P02771.1 AGAP2 Q99490.1 AGO1Q9UL18.1 AGO3 Q9H9G7.1 AGO4 Q9HCK5.1 AGR2 O95994.1 AIFM2 Q9BRQ8.1 AIM2O14862.1 AKAP-13 Q12802.1 AKAP-3 O75969.1 AKAP-4 Q5JQC9.1 AKIP1 Q9NQ31.1AKT1 P31749.1 AKT2 P31751.1 AKT3 Q9Y243.1 ALDH1A1 P00352.1 ALK Q9UM73.1ALKBH1 Q13686.1 ALPK1 Q96QP1.1 AMIGO2 Q86SJ2.1 ANG2 O15123.1 ANKRD45Q5TZF3.1 ANO1 Q5XXA6.1 ANP32A P39687.1 ANXA2 P07355.1 APC P25054.1 APEHP13798.1 APOA2 P02652.1 APOD P05090.1 APOL1 O14791.1 AR P10275.1 ARAFP10398.1 ARF4L P49703.1 ARHGEF5 Q12774.1 ARID3A Q99856.1 ARID4A P29374.1ARL6IP5 O75915.1 ARMC3 B4DXS3.1 ARMC8 Q8IUR7.1 ARTC1 P52961.1 ARXQ96QS3.1 ATAD2 Q6PL18.1 ATIC P31939.1 AURKC Q9UQB9.1 AXIN1 O15169.1 AXLP30530.1 BAAT Q14032.1 BAFF Q9Y275.1 BAGE-1 Q13072.1 BAGE-2 Q86Y30.1BAGE-3 Q86Y29.1 BAGE-4 Q86Y28.1 BAGE-5 Q86Y27.1 BAI1 O14514.1 BALP19835.1 BALF2 P03227.1 BALF4 P03188.1 BALF5 P03198.1 BARF1 P03228.1BBRF1 P03213.1 BCAN Q96GW7.1 BCAP31 P51572.1 BCL-2 P10415.1 BCL2L1Q07817.1 BCL6 P41182.1 BCL9 O00512.1 BCR P11274.1 BCRF1 P03180.1 BDLF3P03224.1 BGLF4 P13288.1 BHLF1 P03181.1 BHRF1 P03182.1 BILF1 P03208.1BILF2 P03218.1 BIN1 O00499.1 BING-4 O15213.1 BIRC7 Q96CA5.1 BLLF1P03200.1 BLLF2 P03199.1 BMI1 P35226.1 BMLF1 Q04360.1 BMPR1B O00238.1BMRF1 P03191.1 BNLF2a P00739.1 BNLF2b Q8AZJ3.1 BNRF1 P03179.1 BRAF1P15056.1 BRD4 O60885.1 BRDT Q58F21.1 BRI3BP Q8WY22.1 BRINP1 O60477.1BRLF1 P03209.1 BTBD2 Q9BX70.1 BUB1B O60566.1 BVRF2 P03234.1 BXLF1P03177.1 BZLF1 P03206.1 C15orf60 Q7Z4M0.1 CA 12-5 Q8WXI7.1 CA 19-9Q969X2.1 CA195 Q5TG92.1 CA9 Q16790.1 CABYR O75952.1 CADM4 Q8NFZ8.1 CAGE1Q8CT20.1 CALCA P01258.1 CALR3 Q96L12.1 CAN P35658.1 CASC3 O15234.1 CASC5Q8NG31.1 CASP5 P51878.1 CASP8 Q14790.1 CBFA2T2 O43439.1 CBFA2T3 O75081.1CBL P22681.1 CBLB Q13191.1 CC3 Q9BUP3.1 CCDC110 Q8TBZ0.1 CCDC33 Q8N5R6.1CCDC36 Q8IYA8.1 CCDC6 Q16204.1 CCDC62 Q6P9F0.1 CCDC68 Q9H2F9.1 CCDC83Q8IWF9.1 CCL13 Q99616.1 CCL2 P13500.1 CCL7 P80098.1 CCNA1 P78396.1 CCNA2P20248.1 CCNB1 P14635.1 CCND1 P24385.1 CCNE2 O96020.1 CCNI Q14094.1CCNL1 Q9UK58.1 CCR2 P41597.1 CD105 P17813.1 CD123 P26951.1 CD13 P15144.1CD133 O43490.1 CD137 Q07011.1 CD138 P18827.1 CD157 Q10588.1 CD16AP08637.1 CD178 P48023.1 CD19 P15391.1 CD194 P51679.1 CD2 P06729.1 CD20P11836.1 CD21 P20023.1 CD22 P20273.1 CD229 Q9HBG7.1 CD23 P06734.1 CD27P26842.1 CD28 P10747.1 CD30 P28908.1 CD317 Q10589.1 CD33 P20138.1 CD350Q9ULW2.1 CD36 P16671.1 CD37 P11049.1 CD4 P01730.1 CD40 P25942.1 CD40LP29965.1 CD45 P08575.1 CD47 Q08722.1 CD51 P06756.1 CD52 P31358.1 CD55P08174.1 CD61 P05106.1 CD70 P32970.1 CD74 P08922.1 CD75 P15907.1 CD79BP40259.1 CD80 P33681.1 CD86 P42081.1 CD8a P01732.1 CD8b P10966.1 CD95P25445.1 CD98 P08195.1 CDC123 O75794.1 CDC2 P06493.1 CDC27 P30260.1CDC73 Q6P1J9.1 CDCA1 Q9BZD4.1 CDCP1 Q9H5V8.1 CDH3 P22223.1 CDK2AP1O14519.1 CDK4 P11802.1 CDK7 P50613.1 CDKN1A P38936.1 CDKN2A P42771.1 CEAP06731.1 CEACAM1 Q86UE4.1 CENPK Q9BS16.1 CEP162 Q5TB80.1 CEP290 O15078.1CEP55 Q53EZ4.1 CFL1 P23528.1 CH3L2 Q15782.1 CHEK1 O14757.1 CK2 P19784.1CLCA2 Q9UQC9.1 CLOCK O15516.1 CLPP Q16740.1 CMC4 P56277.1 CML66 Q96RS6.1CO-029 P19075.1 COTL1 Q14019.1 COX2 P35354.1 COX6B2 Q6YFQ2.1 CPSF1Q10570.1 CPXCR1 Q8N123.1 CREBL2 O60519.1 CREG1 O75629.1 Cripto P13385.1CRISP2 P16562.1 CRK P46108.1 CRKL P46109.1 CRLF2 Q9HC73.1 CSAGE Q6PB30.1CT45 Q5HYN5.1 CT45A2 Q5DJT8.1 CT45A3 Q8NHU0.1 CT45A4 Q8N7B7.1 CT45A5Q6NSH3.1 CT45A6 P0DMU7.1 CT46 Q86X24.1 CT47 Q5JQC4.1 CT47B1 P0C2P7.1CTAGE2 Q96RT6.1 cTAGE5 O15320.1 CTCFL Q8NI51.1 CTDSP2 O14595.1 CTGFP29279.1 CTLA4 P16410.1 CTNNA2 P26232.1 CTNNB1 P35222.1 CTNND1 O60716.1CTSH P09668.1 CTSP1 A0RZH4.1 CTTN Q14247.1 CXCR4 P61073.1 CXorf48Q8WUE5.1 CXorf61 Q5H943.1 Cyclin-E P24864.1 CYP1B1 Q16678.1 CypBP23284.1 CYR61 O00622.1 CS1 P28290.1 CSAG1 Q6PB30.1 CSDE1 O75534.1 CSF1P09603.1 CSF1R P07333.1 CSF3R Q99062.1 CSK P41240.1 CSK23 Q8NEV1.1 DAPK3O43293.1 DAZ1 Q9NQZ3.1 DBPC Q9Y2T7.1 DCAF12 Q5T6F0.1 DCT P40126.1DCUN1D1 Q96GG9.1 DCUN1D3 Q8IWE4.1 DDR1 Q08345.1 DDX3X O00571.1 DDX6P26196.1 DEDD O75618.1 DEK P35659.1 DENR O43583.1 DEPDC1 Q5TB30.1 DFNA5O60443.1 DGAT2 Q96PD7.1 DHFR P00374.1 DKK1 O94907.1 DKK3 Q9UBP4.1 DKKL1Q9UK85.1 DLEU1 O43261.1 DMBT1 Q9UGM3.1 DMRT1 Q9Y5R6.1 DNAJB8 Q8NHS0.1DNAJC8 O75937.1 DNMT3A Q9Y6K1.1 DPPA2 Q7Z7J5.1 DR4 O00220.1 DR5 O14763.1DRG1 Q9Y295.1 DSCR8 Q96T75.1 E2F3 O00716.1 E2F6 O75461.1 E2F8 A0AVK6.1EBNA1 P03211.1 EBNA2 P12978.1 EBNA3 P12977.1 EBNA4 P03203.1 EBNA6P03204.1 EBNA-LP Q8AZK7.1 E-cadherin P12830.1 ECT2 Q9H8V3.1 ECTL2Q00858.1 EDAG Q9BXL5.1 EEF2 P13639.1 EFNA1 P20827.1 EFS O43281.1 EFTUD2Q15029.1 EGFL7 Q9UHF1.1 EGFR p00533.1 EI24 O14681.1 EIF4EBP1 Q13541.1ELF3 P78545.1 ELF4 Q99607.1 ELOVL4 Q9GZR5.1 EMP1 P54849.1 ENAH Q8N8S7.1Endosialin Q9HCU0.1 ENO1 P06733.1 ENO2 P09104.1 ENO3 P13929.1 ENTPD5O75356.1 EpCAM P16422.1 EPHA2 P29317.1 EPHA3 P29320.1 EPHB2 P29323.1EPHB4 P54760.1 EPHB6 O15197.1 EPS8 Q12929.1 ERBB3 P21860.1 ERBB4Q15303.1 EREG O14944.1 ERG P11308.1 ERVK-18 O42043.1 ERVK-19 O71037.1ESR1 P03372.1 ETAA1 Q9NY74.1 ETS1 P14921.1 ETS2 P15036.1 ETV1 P50549.1ETV5 P41161.1 ETV6 P41212.1 EVI5 O60447.1 EWSR1 Q01844.1 EYA2 O00167.1EZH2 Q15910.1 FABP7 O15540.1 FAM133A Q8N9E0.1 FAM13A O94988.1 FAM46DQ8NEK8.1 FAM58BP P0C7Q3.1 FANCG O15287.1 FATE1 Q969F0.1 FBXO39 Q8N4B4.1FBXW11 Q9UKB1.1 FCHSD2 O94868.1 FER P16591.1 FES P07332.1 FEV Q99581.1FGF10 O15520.1 FGF23 Q9GZV9.1 FGF3 P11487.1 FGF4 P08620.1 FGF5 P12034.1FGFR1 P11362.1 FGFR2 P21802.1 FGFR3 P22607.1 FGFR4 P22455.1 FGR P09769.1FLI1 Q01543.1 FLT3 P36888.1 FMNL1 O95466.1 FMOD Q06828.1 FMR1NB Q8N0W7.1FN1 P02751.1 Fn14 Q9NP84.1 FNIP2 Q9P278.1 FOLR1 P15328.1 FOS P01100.1FosB P53539.1 FOSL1 P15407.1 FOXM1 Q08050.1 FOXO1 Q12778.1 FOXO3O43524.1 FRAT1 Q92837.1 FRMD3 A2A2Y4.1 FSIP1 Q8NA03.1 FSIP2 Q5CZC0.1FSTL3 O95633.1 FTHL17 Q9BXU8.1 FUNDC2 Q9BWH2.1 FUS P35637.1 FUT1P19526.1 FUT3 P21217.1 FYN P06241.1 GAB2 Q9UQC2.1 GADD45G O95257.1GAGE-1 Q13065.1 GAGE12B/C/D/E A1L429.1 GAGE12F P0CL80.1 GAGE12G P0CL81.1GAGE12H A6NDE8.1 GAGE12I P0CL82.1 GAGE12J A6NER3.1 GAGE-2 Q6NT46.1GAGE-3 Q13067.1 GAGE-4 Q13068.1 GAGE-5 Q13069.1 GAGE-6 Q13070.1 GAGE-7O76087.1 GAGE-8 Q9UEU5.1 GALGT2 Q00973.1 GAS7 O60861.1 GASZ Q8WWH4.1GATA-3 P23771.1 GBU4-5 Q587J7.1 GCDFP-15 P12273.1 GFAP P14136.1 GFI1Q99684.1 Ghrelin Q9UBU3.1 GHSR Q92847.1 GIPC1 O14908.1 GITR Q9Y5U5.1GKAP1 Q5VSY0.1 GLI1 P08151.1 Glypican-3 P51654.1 GML Q99445.1 GNA11P29992.1 GNAQ P50148.1 GNB2L1 P63244.1 GOLGA5 Q8TBA6.1 gp100 P40967.1gp75 P17643.1 Gp96 P14625.1 GPAT2 Q6NUI2.1 GPATCH2 Q9NW75.1 GPC-3P51654.1 GPNMB Q14956.1 GPR143 P51810.1 GPR89A B7ZAQ6.1 GRB2 P62993.1GRP78 P11021.1 GUCY1A3 Q02108.1 H3F3A P84243.1 HAGE Q9NXZ2.1 hANPP01160.1 HBEGF Q99075.1 hCG-beta P01233.1 HDAC1 Q13547.1 HDAC2 Q92769.1HDAC3 O15379.1 HDAC4 P56524.1 HDAC5 Q9UQL6.1 HDAC6 Q9UBN7.1 HDAC7Q8WUI4.1 HDAC8 Q9BY41.1 HDAC9 Q9UKV0.1 HEATR1 Q9H583.1 Hepsin P05981.1Her2/neu P04626.1 HERC2 O95714.1 HERV-K104 P61576.1 HEXB P07686.1 HEXIM1O94992.1 HGRG8 Q9Y5A9.1 HIPK2 Q9H2X6.1 HJURP Q8NCD3.1 HMGB1 P09429.1HMOX1 P09601.1 HNRPL P14866.1 HOM-TES-85 Q9P127.1 HORMAD1 Q86X24.1HORMAD2 Q8N7B1.1 HPSE Q9Y251.1 HPV16 E6 P03126.1 HPV16 E7 P03129.1 HPV18E6 P06463.1 HPV18 E7 P06788.1 HRAS P01112.1 HSD17B13 Q7Z5P4.1 HSP105Q92598.1 HSP60 P10809.1 HSPA1A P08107.1 HSPB9 Q9BQS6.1 HST-2 P10767.1HT001 Q2TB18.1 hTERT O14746.1 HUS1 O60921.1 ICAM-1 P05362.1 IDH1O75874.1 IDO1 P14902.1 IER3 P46695.1 IGF1R P08069.1 IGFS11 Q5DX21.1IL13RA2 Q14627.1 IMP-3 Q9NV31.1 ING3 Q9NXR8.1 INPPL1 O15357.1 INTS6Q9UL03.1 IRF4 Q15306.1 IRS4 O14654.1 ITGA5 P08648.1 ITGB8 P26012.1 ITPAQ9BY32.1 ITPR2 Q14571.1 JAK2 O60674.1 JAK3 P52333.1 JARID1B Q9UGL1.1JAZF1 Q86VZ6.1 JNK1 P45983.1 JNK2 P45984.1 JNK3 P53779.1 JTB O76095.1JUN P05412.1 JUP P14923.1 K19 P08727.1 KAAG1 Q9UBP8.1 Kallikrein 14Q9P0G3.1 Kallikrein 4 Q9Y5K2.1 KAT6A Q92794.1 KDM1A O60341.1 KDM5AP29375.1 KIAA0100 Q14667.1 KIAA0336 Q8IWJ2.1 KIAA1199 Q8WUJ3.1 KIAA1641A6QL64.1 KIF11 P52732.1 KIF1B O60333.1 KIF20A O95235.1 KIT P10721.1 KLF4O43474.1 KLHL41 O60662.1 KLK10 O43240.1 KMT2D O14686.1 KOC1 O00425.1K-ras P01116.1 KRIT1 O00522.1 KW-12 P62913.1 KW-2 Q96RS0.1 KW-5 (SEBD4)Q9H0Z9.1 KW-7 O75475.1 L1CAM P32004.1 L53 Q96EL3.1 L6 Q9BTT4.1 LAG3P18627.1 Lage-1 O75638.1 LATS1 O95835.1 LATS2 Q9NRM7.1 LCMT2 O60294.1LCP1 P13796.1 LDHC P07864.1 LDLR P01130.1 LEMD1 Q68G75.1 LengsinQ5TDP6.1 LETMD1 Q6P1Q0.1 LGALS3BP Q08380.1 LGALS8 O00214.1 LIN7AO14910.1 LIPI Q6XZE0.1 LIV-1 Q13433.1 LLGL1 Q15334.1 LMO1 P25800.1 LMO2P25791.1 LMP1 P03230.1 LMP2 P13285.1 L00647107 Q8TAI5.1 LOXL2 Q9Y4K0.1LRP1 Q07954.1 LRRN2 O75325.1 LTF P02788.1 LTK P29376.1 LZTS1 Q9Y250.1LY6K Q17RY6.1 LYN P07948.1 LYPD6B Q8NI32.1 MAEA Q7L5Y9.1 MAEL Q96JY0.1MAF O75444.1 MAFF Q9ULX9.1 MAFG O15525.1 MAFK O60675.1 MAGE-A1 P43355.1MAGE-A10 P43363.1 MAGE-A11 P43364.1 MAGE-A12 P43365.1 MAGE-A2 P43356.1MAGE-A2B Q6P448.1 MAGE-A3 P43357.1 MACE-A4 P43358.1 MAGE-A5 P43359.1MAGE-A6 P43360.1 MAGE-A8 P43361.1 MAGE-A9 P43362.1 MAGE-B1 P43366.1MAGE-B2 O15479.1 MAGE-B3 O15480.1 MAGE-B4 O15481.1 MAGE-B5 Q9BZ81.1MAGE-E6 Q8N7X4.1 MAGE-C1 O60732.1 MAGE-C2 Q9UBF1.1 MAGE-C3 Q8TD91.1mammaglobin-A Q13296.1 MANF P55145.1 MAP2K2 P36507.1 MAP2K7 O14733.1MAP3K7 O43318.1 MAP4K5 Q9Y4K4.1 MART1 Q16655.1 MART-2 Q5VTY9.1 MAS1P04201.1 MC1R Q01726.1 MCAK Q99661.1 MCF2 P10911.1 MCF2L O15068.1 MCL1Q07820.1 MCTS1 Q9ULC4.1 MCSP Q6UVK1.1 MDK P21741.1 MDM2 Q00987.1 MDM4O15151.1 ME1 P48163.1 ME491 P08962.1 MECOM Q03112.1 MELK Q14680.1 MEN1O00255.1 MERTK Q12866.1 MET P08581.1 MFGE8 Q08431.1 MFHAS1 Q9Y4C4.1 MFI2P08582.1 MGAT5 Q09328.1 Midkine P21741.1 MIF P14174.1 MKI67 P46013.1MLH1 P40692.1 MLL Q03164.1 MLLT1 Q03111.1 MLLT10 P55197.1 MLLT11Q13015.1 MLLT3 P42568.1 MLLT4 P55196.1 MLLT6 P55198.1 MMP14 P50281.1MMP2 P08253.1 MMP7 P09237.1 MMP9 P14780.1 MOB3B Q86TA1.1 MORC1 Q86VD1.1MPHOSPH1 Q96Q89.1 MPL P40238.1 MRAS O14807.1 MRP1 P33527.1 MRP3 O15438.1MRPL28 Q13084.1 MRPL30 Q8TCC3.1 MRPS11 P82912.1 MSLN Q13421.1 MTA1Q13330.1 MTA2 O94776.1 MTA3 Q9BTC8.1 MTCP1 P56278.1 MTSS1 O43312.1 MUC-1P15941.1 MUC-2 Q02817.1 MUC-3 Q02505.1 MUC-4 Q99102.1 MUC-5AC P98088.1MUC-6 Q6W4X9.1 MUM1 Q2TAK8.1 MUM2 Q9Y5R8.1 MYB P10242.1 MYC P01106.1MYCL P12524.1 MYCLP1 P12525.1 MYCN P04198.1 MYD88 Q99836.1 MYEOVQ96EZ4.1 MYO1B O43795.1 NA88-A P005K6.1 NAE1 Q13564.1 Napsin-A O96009.1NAT6 Q93015.1 NBAS A2RRP1.1 NBPF12 Q5TAG4.1 NCOA4 Q13772.1 NDC80O14777.1 NDUFC2 O95298.1 Nectin-4 NEK2 P51955.1 Q96NY8.1 NEMF O60524.1NENF Q9UMX5.1 NEURL1 O76050.1 NFIB O00712.1 NFKB2 Q00653.1 NF-X1Q12986.1 NFYC Q13952.1 NGAL P80188.1 NGEP Q6IWH7.1 NKG2D-L1 Q9BZM6.1NKG2D-L2 Q9BZM5.1 NKG2D-L3 Q9BZM4.1 NKG2D-L4 Q8TD07.1 NKX3.1 Q99801.1NLGN4X Q8N0W4.1 NLRP4 Q96MN2.1 NNMT P40261.1 NOL4 O94818.1 NOTCH2Q04721.1 NOTCH3 Q9UM47.1 NOTCH4 Q99466.1 NOV P48745.1 NPM1 P06748.1NR6A1 Q15406.1 N-RAS P01111.1 NRCAM Q92823.1 NRP1 O14786.1 NSE1 Q96KN4.1NSE2 Q96KN1.1 NTRK1 P04629.1 NUAK1 O60285.1 NUGGC Q68CJ6.1 NXF2 Q9GZY0.1NXF2B Q5JRM6.1 NY-BR-1 Q9BXX3.1 NYD-TSPG Q9BWV7.1 NY-ESO-1 P78358.1NY-MEL-1 P57729.1 OCA2 Q04671.1 ODF1 Q14990.1 ODF2 Q5BJF6.1 ODF3Q96PU9.1 ODF4 Q2M2E3.1 OGG1 O15527.1 OCT O15294.1 OIP5 O43482.1 OS9Q13438.1 OTOA Q05BM7.1 OX40 P43489.1 OX40L P23510.1 P53 P04637.1 P56-LCKP06239.1 PA2G4 Q9UQ80.1 PAGE1 O75459.1 PAGE2 Q7Z2X2.1 PAGE2B Q5JRK9.1PAGE3 Q5JUK9.1 PAGE4 O60829.1 PAGES Q96GU1.1 PAK2 Q13177.1 PANO1I0J062.1 PAP Q06141.1 PAPOLG Q9BWT3.1 PARK2 O60260.1 PARK7 Q99497.1PARP12 Q9H0J9.1 PASD1 Q8IV76.1 PAX3 P23760.1 PAX5 Q02548.1 PBF P00751.1PBK Q96KB5.1 PBX1 P40424.1 PCDC1 Q15116.1 PCM1 Q15154.1 PCNXL2 A6NKB5.1PDGFB P01127.1 PDGFRA P16234.1 PEPP2 Q9HAU0.1 PGF P49763.1 PGK1 P00558.1PHLDA3 Q9Y5J5.1 PHLPP1 O60346.1 PIAS1 O75925.1 PIAS2 O75928.1 PIK3CAP42336.1 PIK3CD O00329.1 PIK3R2 O00459.1 PIM1 P11309.1 PIM2 Q9P1W9.1PIM3 Q86V86.1 PIR O00625.1 PIWIL1 Q96J94.1 PIWIL2 Q8TC59.1 PIWIL3Q7Z3Z3.1 PIWIL4 Q7Z3Z4.1 PKN3 Q6P5Z2.1 PLA2G16 P53816.1 PLAC1 Q9HBJ0.1PLAG1 Q6DJT9.1 PLEKHG5 O94827.1 PLK3 Q9H4B4.1 PLS3 P13797.1 PLVAPQ9BX97.1 PLXNB1 O43157.1 PLXNB2 O15031.1 PML P29590.1 PML-RARA Q96QH2.1POTEA Q6S8J7.1 POTEB Q6S5H4.1 POTEC B2RU33.1 POTED Q86YR6.1 POTEEQ6S8J3.1 POTEG Q6S5H5.1 POTEH Q6S545.1 PP2A P63151.1 PPAPDC1B Q8NEB5.1PPFIA1 Q13136.1 PPIG Q13427.1 PPP2R1B P30154.1 PRAME P78395.1 PRDX5P30044.1 PRKAA1 Q13131.1 PRKCI P41743.1 PRM1 P04553.1 PRM2 P04554.1PRMT3 O60678.1 PRMT6 Q96LA8.1 PDL1 Q9NZQ7.1 PROM1 O43490.1 PRSS54Q6PEW0.1 PRSS55 Q6UWB4.1 PRTN3 P24158.1 PRUNE Q86TP1.1 PRUNE2 Q8WUY3.1PSA P07288.1 PSCA D3DWI6.1 PSMA Q04609.1 PSMD10 O75832.1 PSGR Q9H255.1PSP-94 Q1L6U9.1 PTEN P60484.1 PTH-rP P12272.1 PTK6 Q13882.1 PTPN20AQ4JDL3.1 PTPRK Q15262.1 PTPRZ P23471.1 PTTG-1 O95997.1 PTTG2 Q9NZH5.1PTTG3 Q9NZH4.1 PXDNL A1KZ92.1 RAB11FIP3 O75154.1 RAB8A P61006.1 RAD1O60671.1 RAD17 O75943.1 RAD51C O43502.1 RAF1 P04049.1 RAGE-1 Q9UQ07.1RAP1A P62834.1 RARA P10276.1 RASSF10 A6NK89.1 RB1 P06400.1 RBL2 Q08999.1RBM46 Q8TBY0.1 RBP4 P02753.1 RCAS1 O00559.1 RCVRN P35243.1 RECQL4O94761.1 RET P07949.1 RGS22 Q8NE09.1 RGS5 O15539.1 RHAMM O75330.1 RhoCP08134.1 RHOXF2 Q9BQY4.1 RL31 P62888.1 RNASET2 O00584.1 RNF43 Q68DV7.1RNF8 O76064.1 RON Q04912.1 ROPN1A Q9HAT0.1 ROR1 Q01973.1 RPA1 O95602.1RPL10A P62906.1 RPL7A P62424.1 RPS2 P15880.1 RPS6KA5 O75582.1 RPSAP08865.1 RQCD1 Q92600.1 RRAS2 P62070.1 RSL1D1 O76021.1 RTKN Q9BST9.1RUNX1 Q01196.1 RUNX2 Q13950.1 RYK P34925.1 SAGE1 Q9NXZ1.1 SART2 Q9UL01.1SART3 Q15020.1 SASH1 O94885.1 sCLU P10909.1 SCRN1 Q12765.1 SDCBPO00560.1 SDF-1 P48061.1 SDHD O14521.1 SEC31A O94979.1 SEC63 Q9UGP8.1Semaphorin 4D Q92854.1 SEMG1 P04279.1 SFN P31947.1 SH2B2 O14492.1 SH2D1BO14796.1 SH3BP1 Q9Y3L3.1 SHE Q15464.1 SHC3 Q92529.1 SIRT2 Q8IXJ6.1 SIVA1O15304.1 SKI P12755.1 SLBP A9UHW6.1 SLC22A10 Q63ZE4.1 SLC25A47 Q6Q0C1.1SLC35A4 Q96G79.1 SLC45A3 Q96JT2.1 SLC4A1AP Q9BWU0.1 SLCO6A1 Q86UG4.1SLITRK6 Q9H5Y7.1 Sm23 P27701.1 SMAD5 Q99717.1 SMAD6 O43541.1 SMOQ99835.1 Smt3B P61956.1 SNRPD1 P62314.1 SOS1 Q07889.1 SOX-2 P48431.1SOX-6 P35712.1 SOX-11 P35716.1 SPA17 Q15506.1 SPACA3 Q8IXA5.1 SPAG1Q07617.1 SPAG17 Q6Q759.1 SPAG4 Q9NPE6.1 SPAG6 O75602.1 SPAG8 Q99932.1SPAG9 O60271.1 SPANXA1 Q9N526.1 SPANXB Q9N525.1 SPANXC Q9NY87.1 SPANXDQ9BXN6.1 SPANXE Q8TAD1.1 SPANXN1 Q5VSR9.1 SPANXN2 Q5MJ10.1 SPANXN3Q5MJ09.1 SPANXN4 Q5MJ08.1 SPANXN5 Q5MJ07.1 SPATA19 Q7Z5L4.1 SPEF2Q9C093.1 SPI1 P17947.1 SPINLW1 O95925.1 SPO11 Q9Y5K1.1 SRC P12931.1 SSPNQ14714.1 SSX-1 Q16384.1 SSX-2 Q16385.1 SSX-3 Q99909.1 SSX-4 O60224.1SSX-5 O60225.1 SSX-6 Q7RTT6.1 SSX-7 Q7RTT5.1 SSX-9 Q7RTT3.1 ST18O60284.1 STAT1 P42224.1 STEAP1 Q9UHE8.1 STK11 Q15831.1 STK25 O00506.1STK3 Q13188.1 STN Q9H668.1 SUPT7L O94864.1 Survivin O15392.1 SUV39H1O43463.1 SYCE1 Q8N052.1 SYCP1 Q15431.1 SYCP3 Q8IZU3.1 SYT Q15532.1 TA-4Q96RI8.1 TACC1 O75410.1 TAF1B Q53T94.1 TAF4 O00268.1 TAF7L Q5H9L4.1TAG-1 Q02246.1 TAL1 P17542.1 TAL2 Q16559.1 TAPBP O15533.1 TATI P00995.1TAX1BP3 O14907.1 TBC1D3 Q8IZP1.1 TBP-1 P17980.1 TCL1A P56279.1 TCL1BO95988.1 TDHP Q9BT92.1 TDRD1 Q9BXT4.1 TDRD4 Q9BXT8.1 TDRD6 O60522.1TEKT5 Q96M29.1 TEX101 Q9BY14.1 TEX14 Q8IWB6.1 TEX15 Q9BXT5.1 TEX38Q6PEX7.1 TF P02787.1 TFDP3 Q5H9I0.1 TFE3 P19532.1 TGFBR1 P36897.1 TGFBR2P37173.1 THEG Q9P2T0.1 TIE2 Q02763.1 TIPRL O75663.1 TLR2 O60603.1 TMEFF1Q8IYR6.1 TMEFF2 Q9UIK5.1 TMEM108 Q6UXF1.1 TMEM127 O75204.1 TMPRSS12Q86W55.1 TNC P24821.1 TNFRSF17 Q02223.1 TNFSF15 O95150.1 TNK2 Q07912.1TOMM34 Q15785.1 TOP2A P11388.1 TOP2B Q02880.1 TOR3A Q9H497.1 TP73O15350.1 TPA1 8N543.1 TPGS2 Q68CL5.1 TPI1 P60174.1 TPL2 P41279.1 TPM4P67936.1 TPO P40225.1 TPPP2 P59282.1 TPR P12270.1 TPTE P56180.1 TRAF5O00463.1 TRAG-3 Q9Y5P2.1 TRGC2 P03986.1 TRIM24 O15164.1 TRIM37 O94972.1TRIM68 Q6AZZ1.1 TRPM8 Q7Z2W7.1 TSGA10 Q9BZW7.1 TSP50 Q9UI38.1 TSPAN6O43657.1 TSPY1 Q01534.1 TSPY2 A6NKD2.1 TSPY3 Q6B019.1 TSPYL1 Q9H0U9.1TSSK6 Q9BXA6.1 TTC23 Q5W5X9.1 TTK P33981.1 TULP2 O00295.1 TUSC2 O75896.1TWEAK O43508.1 TXNIP Q9H3M7.1 TYMS P04818.1 TYR P14679.1 U2 snRNP BP08579.1 U2AF1 Q01081.1 UBD O15205.1 UBE2A P49459.1 UBE2C O00762.1UBE2V1 Q13404.1 UBE4B O95155.1 UBR5 O95071.1 UBXD5 Q5T124.1 UFL1O94874.1 URI1 O94763.1 URLC10 Q17RY6.1 UROC1 Q96N76.1 USP2 O75604.1 USP4Q13107.1 VAV1 P15498.1 VCX3A Q9NNX9.1 VEGFR1 P17948.1 VEGFR2 P35968.1VHL P40337.1 VIM P08670.1 VWA5A O00534.1 WHSC2 Q9H3P2.1 WISP1 O95388.1WNK2 Q9Y351.1 WNT10B O00744.1 WNT3 P56703.1 WNT-5a P41221.1 WT1 P19544.1WWP1 Q9HOM0.1 XAGE-1 Q9HD64.1 XAGE-2 Q96GT9.1 XAGE-3 Q8WTP9.1 XAGE-4Q8WWM0.1 XAGE-5 Q8WWM1.1 XBP1 P17861.1 XPO1 O14980.1 XRCC3 O43542.1 YB-1P67809.1 YEATS4 O95619.1 YES1 P07947.1 YKL-40 P36222.1 ZBTB7A O95365.1ZBTB7C A1YPR0.1 ZEB1 P37275.1 ZFYVE19 Q96K21.1 ZNF165 P49910.1 ZNF185O15231.1 ZNF217 O75362.1 ZNF320 A2RRD8.1 ZNF395 Q9H8N7.1 ZNF645 Q8N7E2.1ZUBR1 Q5T4S7.1 ZW10 O43264.1 ZWINT O95229.1

TABLE 3 LIST OF ACCESSION NUMBERS FOR VIRAL ANTIGENS FROM IEDB Q76R62.1P03182.1 P09258.1 P09310.1 P03227.1 P89466.1 P04601.1 P13285.1 P09991.1P03468.1 A2T3Q0.1 P0C6X7.1 P89448.1 P12978.1 P09257.1 P50641.1 P14075.120178567.1 Q01023.1 P03188.1 P04585.1 P00767.1 P12977.1 P89467.1Q9W850.1 Q00683.1 P04591.1 P03211.1 9628706.1 P03460.1 P08666.1 P03485.1Q04360.1 Q913Y7.1 P89449.1 Q81871.1 P03452.1 P17763.1 P89430.1 P03410.1P04012.1 P27958.1 Q6WB99.1 P25212.1 Q9PZT1.1 P68593.1 P03203.1 P29996.19629374.1 P59633.1 O42053.1 P0C6L3.1 P59635.1 Q9YZN9.1 Q6WB95.1 P10233.1P89475.1 Q6WB98.1 Q6SW67.1 Q7TFA0.1 P0CK17.1 P59594.1 1980491.1 P14079.1P15423.1 1891762.1 P09259.1 P09269.1 Q77Q38.1 Q786F2.1 Q6SW99.1 P24771.1F5HB98.1 9629370.1 P68336.1 P03300.1 1980486.1 Q69027.1 P28284.1P13290.1 9626585.1 P06923.1 P14076.1 P03346.1 O42062.1 P07566.1 P03204.1Q69091.1 P09255.1 P03206.1 O36634.1 P10205.1 F5HCM1.1 P0CK16.1 Q6WB97.1Q85601.1 P89468.1 Q69467.1 P03218.1 Q786F3.1 P59637.1 1891763.1 Q6WB94.1P03231.1 Q91K92.1 Q6WBA1.1 P03466.1 P14335.1 P26670.1 Q9PZT0.1 1985356.1Q2HR63.1 P59634.1 Q6SW59.1 P03277.1 P59595.1 Q69028.1 P03383.1 P03261.1P03200.1 P04578.1 P06484.1 F5HC97.1 S5TC82.1 P18095.1 Q96895.1 P18094.19629372.1 P50791.1 P03230.1 P13845.1 9629712.1 P03209.1 P03129.1Q76R61.1 P03228.1 P0C206.1 Q9WMB5.1 P03226.1 Q9QR69.1 O36633.1 O42049.1P03496.1 P03428.1 P03431.1 P0C0U1.1 P03433.1 P03508.1 1980456.1 P00739.1P69726.1 P69723.1 1980490.1 532129755.1 P03120.1 P04020.1 P06922.1P03114.1 P03314.1 P06790.1 P06788.1 P06927.1 P03101.1 P03107.1 P06794.1530787712.1 P04013.1 Q80872.1 P04014.1 P03126.1 P36811.1 P06463.1P26554.1 P04016.1 P14078.1 P03191.1 1980471.1 P06821.1 P00797.1 F5HF49.1P00045.1 P04296.1 P04485.1 P10230.1 P10221.1 P06487.1 P10215.1 P04293.1P10211.1 P10209.1 P10225.1 P10224.1 P10238.1 P10185.1 P08392.1 P10231.1P06492.1 P04290.1 P08393.1 P08543.1 P10210.1 P08617.1 F5HB53.1 P04019.1P04015.1 P89442.1 P89452.1 P89462.1 P59632.1 O36635.1 P07210.1 Q83884.1Q8JUX5.1 P03089.1 Q66479.1 P03185.1 P0CAP6.1 P04618.1 56160929.11980519.1 P08669.1 P14348.1 P03212.1 P03179.1 45617- 1511872.1302317869.1 P69899.1 P09247.1 Q05127.1 P18272.1 other.1 Q9YMG2.1Q05128.1 302371215.1 302371218.1 Q5XX08.1 302371214.1 P14336.1 138948-other.1 P08292.1 1803956.1 P35253.1 1891726.1 P09308.1 P03189.1667489389.1 P09272.1 34365530.1 Q05320.1 P59596.1 P32886.1 55097.1P03316.1 P03276.1 Q81870.1 Q81862.1 64320.1 1933190.1

TABLE 4 LIST OF ACCESSION NUMBERS FOR BACTERIAL ANTIGENS FROM IEDBB8ZUD1.1 P09621.1 P9WPE5.1 Q2GI62.1 P0A5B8.1 O50443.1 Q5NEZ3.1 P9WQF5.1P9WK95.1 O05311.1 P9WQD7.1 P9WKG3.1 P9WHE5.1 P0CD83.1 P9WHB9.1 P9WH91.1P9WHE3.1 P9WNK7.1 A0A0F3MKF3.1 A1JIP3.1 B2RKS6.1 P0A1D3.1 P0A6F5.1P0C0Z7.1 P0C923.1 P61439.1 Q9Z708.1 P0A521.1 P9WPE7.1 Q79FJ2.1 B8ZR84.1I6Y3P5.1 Q2FYP2.1 P9WG41.1 P96890.1 O06625.1 I6X654.1 Q8YIE1.1 P9WQ81.1I6XWA1.1 P11311.1 O53900.1 P9WIR7.1 P9WQB1.1 B8ZUC6.1 O06802.1 P9WMK1.1P9WG37.1 Q2FWC4.1 Q2GGE3.1 O33347.1 P9WJ09.1 P9WJ11.1 P9WF23.1 O69703.1I6X4K0.1 B2RM93.1 P71888.1 P9WFW3.1 P9WPV1.1 P9WPU7.1 P9WPV3.1 P9WPU5.1O50391.1 P9W1D7.1 P9WPC3.1 P96901.1 O84848.1 Q2FUX4.1 A0A0M1YNY3.1P49944.1 P9WPQ9.1 Q45010.1 Q2FZK7.1 P9WMN3.1 P9WPQ1.1 Q45013.1 O53666.1Q5NEH1.1 P9WHR5.1 P9WIE5.1 Q5NEQ3.1 P9WNF3.1 F2QBN0.1 B8ZTB7.1 P0C922.1P9WMJ9.1 Q5NGW2.1 P01556.1 Q8DMZ4.1 P33768.1 Q2FUY2.1 Q5NG56.1 X8CE55.1Q5NGE4.1 P94973.1 O06827.1 P96872.1 I6X9Y7.1 I6XFZ8.1 O50442.1 O53697.1O53978.1 P95137.1 P95144.1 O53519.1 Q79FZ8.1 P9WJF5.1 P71629.1 P9WJS3.1P9WPB7.1 Q7D9T1.1 P9WHS1.1 O06393.1 P9WP69.1 P9WPN5.1 P9WNX3.1 O53380.1I6YAU3.1 P0A4V2.1 P9WQP3.1 P0C2T2.1 P9WQP1.1 P9WQN9.1 O53311.1 P9WIS7.1O06159.1 H2GU79.1 Q2G2Q0.1 P9WNV1.1 P9WNV5.1 Q8YE98.1 Q59191.1 P9WGY7.1P9WGY9.1 Q2G2W1.1 P9WGH1.1 P9WNG9.1 P9WNG7.1 O84591.1 Q9Z7A6.1 P9WGR1.1P96404.1 I6YGS0.1 Q6MX18.1 P9WNK5.1 053692.1 P9WNK3.1 P9WNK1.1 P9WNJ9.1P9WNJ7.1 P9WNJ5.1 P9WNJ3.1 P9WNJ1.1 P9WNI9.1 P96903.1 P9WNB1.1 P9WJE1.1P9WJD9.1 P9WJD7.1 P9WJD3.1 P9WJC5.1 P9WJC3.1 P9WJC1.1 P9WNQ3.1 P9WJE5.1P9WJC7.1 O84646.1 I6YDV4.1 P11439.1 Q5NFJ1.1 P9WNE5.1 P14738.1 P11089.1H7C7G3.1 L7N6B9.1 16XFI7.1 O05578.1 P96218.1 P9WN39.1 P9WN59.1 Q8YBI3.1P9WN83.1 P9WJA9.1 P9WMY9.1 Q5NH51.1 O53673.1 P9WIP9.1 P0CE15.1 P72041.1Q5NEM8.1 Q5NI16.1 P9WJA3.1 P0A4Q1.1 P9WIP1.1 P9WIN9.1 P9WNF5.1 O50846.1Q59947.1 H7C7N8.1 Q5NEC6.1 O84606.1 P9WQJ9.1 P9WQJ7.1 P9WQ71.1 O53611.1P9WKL1.1 P9WKJ7.1 D5V9Y8.1 P0CC04.1 P23700.1 P9WJN5.1 Q5NHJ0.1 Q5NEY9.1P15917.1 Q2G155.1 O34094.1 Q8F8E1.1 O69661.1 H6MMU4.1 P9WK61.1 P9WK55.1Q8YGS9.1 O50811.1 P9WQ59.1 P9WIN7.1 P9WIR1.1 O50430.1 D5VCH6.1 Q5NHI7.1P9WFU9.1 I6XFY8.1 B2RH54.1 Q46409.1 P30690.1 A0A0J5IWN3.1 A0PSI5.1A4TAC4.1 B1MB69.1 B2HSY2.1 B8ZSN3.1 E4WHS0.1 P9WK17.1 V5XE39.1 I6X7G8.1I6Y461.1 I6YGB1.1 I6YC99.1 Q79FY7.1 I6X5Z8.1 I6Y479.1 I6YA32.1 O05461.1Q2G1E2.1 P9WK19.1 I6YAW3.1 Q5NGG4.1 O51624.1 P9WJW5.1 Q50584.1 B2RHG1.1Q5NFL7.1 P9WQN7.1 P9WHH3.1 O84639.1 Q5NF24.1 P9WJH1.1 P9WJH5.1 O53203.1P55969.1 O50418.1 Q5NGE0.1 H7C7K8.1 O54584.1 G1UB30.1 Q5NH85.1 G1UB25.1P0A3N8.1 E1X6Y5.1 Q5NEP7.1 Q8YHH0.1 P38006.1 P43838.1 P43839.1 P0CL67.1P0CL66.1 Q0SLZ0.1 Q07337.1 G5IX16.1 O07721.1 O53254.1 P75330.1 I6Y936.1L7N649.1 L7N656.1 L7N693.1 Q79FK4.1 Q79FR3.1 Q79FR5.1 Q79G04.1 Q79FS8.1Q6MWX1.1 Q79FV6.1 Q79FS5.1 Q79FQ7.1 Q79FP3.1 Q79FP2.1 Q79FK9.1 Q79FE6.1I6XEF1.1 Q79FD4.1 Q6MX26.1 Q6MX50.1 L7N680.1 O53695.1 I6X8R2.1 O53246.1I6Y0L1.1 Q2G282.1 P14283.1 P04977.1 P9WMX7.1 P9WFR1.1 P9WN09.1 O86345.1P9WGU1.1 P9WGT9.1 P9WGT7.1 P9WPF7.1 P9WIB3.1 P9WMM9.1 P9WHM5.1 P9WQE9.1Q8DQ08.1 Q8DQ07.1 I6Y231.1 P9WHV9.1 O05877.1 O07236.1 O86370.1 O06404.1O06410.1 B8ZRL2.1 O06807.1 O33269.1 Q79FA9.1 Q79FK6.1 Q8VKN2.1 L7N675.1Q79FK5.1 L0T7Y7.1 Q79F19.1 Q79FE1.1 Q6MWX9.1 O84616.1 O84647.1 P9WQ27.1O84288.1 I6X9S5.1 P9WJW3.1 P9WPS9.1 P95149.1 O53632.1 I6Y293.1 L0T243.1P9WP43.1 P9WKC9.1 P96402.1 P71810.1 O06417.1 P96365.1 L0T5B2.1 P96264.1P9WJK5.1 P9WJQ9.1 O84419.1 O84818.1 Q8YG32.1 O06608.1 O07175.1 P9WGA3.1O53323.1 P96354.1 P9WIM9.1 B8ZRT2.1 P9WK93.1 P13423.1 O84583.1 P9WG63.1P9WIM1.1 P9WKJ3.1 P9WNZ7.1 P9WK31.1 Q50701.1 P9WID3.1 Q8YC41.1 P9WPL3.1P9WNI3.1 P9WNI7.1 P9WNI5.1 P9WQ49.1 P9WMG1.1 Q2GGR3.1 P9WK71.1 O33192.1P9WND5.1 P9WFL9.1 P9WMB7.1 P9WJ79.1 P9WND7.1 Q63RA7.1 Q631D0.1 I6YET7.1Q9S010.1 P9WGC9.1 Q50700.1 Q5NFR6.1 P9WGK3.1 P9WHI1.1 P9WHV3.1 Q5NIA7.1P9WG27.1 P9WF73.1 P9WGA1.1 P9WIB9.1 P9WGL3.1 O51381.1 P9WI83.1 P9WI79.1P9WFT7.1 Q8YGS6.1 P05788.1 P17835.1 P9WIK9.1 Q5NHP7.1 P9WJU5.1 P9WGE7.1Q2G2B2.1 P04958.1 P9WG67.1 P9WKE1.1 O07226.1 P9WJ13.1 P9WHF3.1 P9WF43.1Q7D7L0.1 P9WMF9.1 P9WGN1.1 P9WKJ9.1 P60230.1 P9WKH7.1 O53699.1 P9WHT7.1P9WJS5.1 Q5NII0.1 Q8YDZ3.1 Q9RPX7.1 P9WN67.1 O05576.1 Q5NHL4.1 P9WN15.1P9WMD5.1 P9WMF5.1 P9WG85.1 P9WJW7.1 P9WIH1.1 P9WIG1.1 P9WIG3.1 P9WIF5.1P9WIF1.1 P9WIE7.1 P9WHW9.1 P9WI41.1 P9WI39.1 P9WI37.1 P9WI25.1 Q11031.1P9WI47.1 P9WI23.1 P9WI19.1 P9WI11.1 P9WI45.1 P9WI07.1 P9WI05.1 Q79FH3.1P9WI43.1 P9WHZ7.1 P9WHZ5.1 P9WHZ3.1 P9WHY9.1 P9WHY7.1 P9WHY5.1 Q6MX07.1P9WHY3.1 Q6MWY2.1 Q50703.1 P9WHX3.1 P96221.1 Q7D589.1 P9WMA3.1 P9WKW1.1P9WKS9.1 P9WM29.1 P9WGC1.1 P9WLZ5.1 P9WLZ3.1 P9WLX1.1 P9WLV9.1 P9WLS7.1P9WLQ1.1 P9WLJ1.1 P9WLH9.1 P9WLF3.1 P9WL97.1 P9WL87.1 P9WL85.1 P9WL83.1P9WL67.1 P9WL63.1 P9WL51.1 P9WL47.1 P9WNH3.1 P9WGL7.1 P9WQM5.1 P9WPD9.1A0A098A1N7.1 A0A098A2B0.1 A2RGM0.1 A5LVF6.1 A5MKZ9.1 B8ZQI8.1 B8ZQM3.1B8ZQT5.1 B8ZR82.1 B8ZRH1.1 B8ZS71.1 B8ZS85.1 B8ZS86.1 B8ZSJ5.1 B8ZSL3.1B8ZSL7.1 B8ZSM6.1 B8ZT30.1 B8ZTD0.1 B8ZTS2.1 B8ZTV5.1 B8ZU53.1 B8ZUA4.1B8ZUE5.1 B8ZUF0.1 B8ZUT6.1 B8ZUX6.1 C0R9U8.1 C6DPT8.1 C6DQ35.1 E1XJN6.1G8W6L3.1 G8W6L7.1 G8W6U7.1 H6MNY3.1 H6MQD5.1 H8HRN0.1 H8HW90.1 H8L8K3.1I6TQ53.1 I6TX52.1 P005B9.1 Q1BYS7.1 R4MDK6.1 S5F815.1 W6GWM1.1 P9WFC9.1P9WFJ9.1 P14916.1 P69996.1 P9WFC5.1 Q8VKQ6.1 P9WHS3.1 A5MKI6.1

TABLE 5 LIST OF ACCESSION NUMBERS FOR FUNGAL ANTIGENS FROM IEDB andUNIPROT Q5ANA3.1 Q5A3P6.1 Q59VM7.1 Q5A1A9.1 Q5APF0.1 Q8J0P4.1 Q4WHG0.1Q4WQ87.1 Q59X67.1 Q59Z17.1 Q59ZI3.1 Q5AA33.1 B8N4Q9.1 Q4WAW6.1 Q4WAJ6.1Q4X1V0.1 A0A1D8PQ86.1 Q59ZB1.1 Q873N2.1 Q59L72.1 B8NIF0.1 P46075.1Q4WCL1.1 Q4WRP2.1 Q59L12.1 Q59LC9.1 P48989.1 Q5AFC2.1 B8N406.1 Q4WGL5.1Q9HEQ8.1 Q4WVI6.1 P46593.1 P82611.1 Q5ADV5.1 Q59SG9.1 P41750.1 O00092.1Q4WEN1.1 Q4WCV3.1 P0DJ06.1 O94038.1 Q59WD3.1 Q59RQ0.1 B8NM71.1 Q4WLW8.1Q4WI37.1 Q4WNI1.1 P29717.1 P46589.1 Q59W04.1 Q59RK9.1 B8MYS6.1 Q8X176.1Q4WZS1.1 Q4WQH4.1 Q9UW14.1 Q5AF56.1 Q59VN0.1 P31353.1 B8N8Q9.1 Q96UX3.1Q4WDA4.1 Q4WDE1.1 Q92207.1 P83773.1 Q59WB9.1 Q5ACM4.1 B8N8R3.1 Q4WPF5.1Q4WLS7.1 Q4WJT7.1 Q5A8T7.1 Q59YU1.1 Q59P53.1 Q5ACI8.1 B8N417.1 Q92450.1Q4WWM6.1 Q4WLG1.1 Q5A8T4.1 Q59YV2.1 Q5A432.1 Q5AB93.1 B8N8R0.1 Q4WAW9.1Q4WP81.1 Q4WQR6.1 P43076.1 Q5ABE5.1 Q5AK64.1 Q5ALL8.1 B8NM74.1 A4GYZ0.1Q6MYT0.1 Q4WZS2.1 Q5AP53.1 Q59LF2.1 A0A1D8PNZ7.1 Q5A4X8.1 B8N106.1Q4WAW3.1 Q4WTL0.1 Q4WXP0.1 Q5AL52.1 Q8NJN3.1 Q59Q30.1 Q5AD34.1 B8NHY4.1Q70J59.1 Q4WXV2.1 Q4WU59.1 P43079.1 Q5ALN1.1 A0A1D8PN12.1 Q59V02.1B8NJG8.1 Q4X1A4.1 Q4X0Z3.1 Q4WUG4.1 Q5AD07.1 Q59572.1 Q5AK24.1 Q5AHC0.1B8NM66.1 E9R876.1 Q4WN25.1 Q4WIK9.1 Q5A0E5.1 Q59K86.1 Q5AFT2.1 Q59Y11.1B8MYL0.1 M4VQY9.1 Q4WN21.1 Q4WYP0.1 Q5AKU6.1 Q5AGD1.1 Q5A0W6.1 Q59QA5.1B8NM62.1 Q4WF53.1 Q4X1N0.1 Q4X0B5.1 Q59RL7.1 P79023.1 P0CB63.1 Q5AMJ5.1B8NGT5.1 Q4WZ64.1 Q4WQV2.1 Q4WYK9.1 G1UB61.1 Q59LP6.1 Q59U11.1 Q5AMF7.1B8NM64.1 Q4WAZ0.1 Q4WZP2.1 Q4WY33.1 Q5ABC6.1 Q5AP87.1 P83775.1 Q5ABW2.1B8NV37.1 Q4WR16.1 Q4WVK2.1 Q4X1F8.1 A0A1D8PQB9.1 P22274.1 Q5APF2.1Q5APJ9.1 B8N151.1 Q4WLB9.1 Q4WUA0.1 Q4WA45.1 P87020.1 Q5AC48.1 Q59VP2.1Q5AM72.1 B8NEJ3.1 Q4WQS0.1 A4DA84.1 Q4WKD7.1 P0CY27.1 Q5AP59.1 Q5AEE1.1Q5ACU3.1 B8N8M2.1 Q4WEP7.1 Q4WJX0.1 Q4WCH5.1 Q59XX2.1 Q59MV1.1 Q5AMR5.1Q5A1V3.1 B8MYV0.1 E9R9Y3.1 Q4WP38.1 Q4WXY3.1 Q59U10.1 Q5AL27.1 Q59SU5.1Q59RF7.1 B8N717.1 P41748.1 Q4X1D7.1 Q4WPL7.1 Q59RW5.1 Q5AJD2.1 Q59VP1.1Q5ACN3.1 B8NJG3.1 Q4WYG3.1 Q4W9Z9.1 Q4X136.1 Q59MQ0.1 P0CU38.1 Q5ADQ0.1Q5AHE8.1 B8N8R1.1 P87184.1 Q4WE62.1 Q4WZ44.1 Q5ABU7.1 Q59QC5.1 Q5AK59.1Q5AHA4.1 B8NJH2.1 Q4WBS1.1 Q4WZL3.1 Q4WTC7.1 Q9Y7F0.1 Q5A5N6.1 Q59RH5.1Q5AEG7.1 B8NQ51.1 Q70DX9.1 Q4WB37.1 Q4WMK2.1 Q5AC08.1 Q59Q79.1 Q5ACW8.1Q59V01.1 B8NM63.1 Q4WG16.1 Q4W9Z4.1 Q4WNC9.1 P30575.1 Q5AH38.1 Q5AGM0.1Q5AK97.1 B8NM73.1 Q96X30.1 Q4WDD0.1 Q4WY67.1 Q5AAG6.1 Q5AMN3.1 Q59VN2.1Q5A1B2.1 B8NYX0.1 Q4WV19.1 Q4WKB9.1 Q4WU12.1 O74189.1 Q5A1Z5.1 O94069.1Q5AJK6.1 B8N3P7.1 Q4WAZ6.1 Q4WU07.1 Q4WA61.1 Q59W62.1 Q5A6K2.1 P0CY20.1Q59L96.1 B8NJH1.1 Q4W944.1 Q4WBL6.1 Q4WA58.1 P0CY34.1 Q59L25.1 Q59XQ1.1Q59MD0.1 B8MXJ7.1 Q4WTV7.1 Q4WX13.1 Q4WA60.1 Q5A1D3.1 Q5A922.1 O94048.1Q5AG46.1 B8NJB0.1 Q4WMJ9.1 Q4WV71.1 Q4WX36.1 Q5AJU7.1 Q5AFG1.1 Q5ADX2.1Q59VW6.1 B8NPS7.1 Q4WZ65.1 Q4X0C2.1 Q4WA62.1 Q5A4H5.1 Q5ALR8.1 P46586.1Q5A8I6.1 B8N7Z8.1 A0A067Z9B6.1 Q4WRU4.1 Q4WA59.1 Q59Y31.1 Q5AEI2.1P83776.1 Q9UW24.1 B8NSV5.1 Q66WM4.1 Q4WGS4.1 Q4WXQ7.1 P0CY29.1 Q5AI71.1Q5A895.1 Q59Q38.1 B8MZA3.1 Q6T267.1 Q4WP13.1 Q4WVA0.1 Q5ANJ4.1 Q5ABA6.1Q59PP0.1 Q5ADL0.1 B8NLY9.1 Q4WLW5.1 Q4WHG5.1 Q4WDN4.1 Q59NH8.1 Q5ABX0.1Q5AHH4.1 Q5AH11.1 B8NR69.1 Q4WMJ0.1 Q4WPF7.1 Q4WK03.1 P0CY33.1 Q5A4N0.1Q96UX5.1 Q59W55.1 B8MZ41.1 Q4WQU0.1 Q4WH83.1 Q4WCG2.1 Q00310.1 Q59TN9.1P87206.1 Q5AC37.1 B8N7S7.1 Q4WMJ8.1 Q4WXW1.1 Q4WX99.1 Q5A0W9.1 Q5A557.1Q5A029.1 Q5A7Q3.1 B8NR71.1 Q4WWW8.1 Q8NJM2.1 Q4WV10.1 Q5A4M8.1 Q59UG3.1Q5A1E0.1 Q59PV6.1 A0A0D9MRV9.1 Q4WZ63.1 Q4WWD3.1 Q4WIS6.1 Q5AJC0.1P0C075.1 Q59XL0.1 P0CH96.1 P55790.1 Q4WVN4.1 Q4WPU8.1 Q4WP65.1 Q595U1.1Q59R09.1 Q5A6U1.1 P83782.1 B8NM72.1 Q4WAY8.1 Q4WN99.1 Q4WUK1.1 Q5AG71.1Q9B8D4.1 Q5A8I8.1 Q5A660.1 B8MW78.1 Q4WY07.1 P0C959.1 Q4WKN3.1 Q5AMT2.1Q9B8D3.1 Q59PR9.1 Q59YT1.1 Q9P900.1 Q4WZ66.1 Q4X0S7.1 Q4WG58.1 Q59KY8.1Q9B8D5.1 O74261.1 P53709.1 B8NDE2.1 Q4WQZ5.1 Q4WPW2.1 Q4WXX9.1 Q59LY1.1Q59LR2.1 Q96VB9.1 Q5ACX1.1 B8NJF4.1 O42630.1 Q4X1U0.1 Q4WC37.1 Q59UT4.1Q5AED9.1 Q5AQ47.1 Q5ADP9.1 B8NIV9.1 P0C7S9.1 Q4WP57.1 Q4X1Y0.1 Q5ABC5.1Q5A4W8.1 Q5A985.1 Q92210.1 B8NG16.1 Q4WI46.1 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Q4WRQ7.1 Q4WMS9.1Q4WXD3.1 Q5AH02.1 Q59PR3.1 Q5AI97.1 Q5AHK2.1 B8NJG7.1 Q4WTQ6.1 Q4WAH4.1Q4WJ02.1 Q5A4X5.1 Q5A2W2.1 Q5A2A2.1 Q5ADP6.1 B8N7Z6.1 Q4WJ21.1 Q4WI13.1Q4WP96.1 Q5A4E3.1 Q5A4E2.1 Q5A044.1 Q5AK62.1 B8NGU1.1 Q4WPQ8.1 Q4WJA1.1Q4WN54.1 Q5A761.1 Q5A309.1 Q59P03.1 Q59YF0.1 B8NC10.1 Q4WR62.1 Q4W9R7.1Q4WCW2.1 Q9UW23.1 A0A1D8PL26.1 Q59TU0.1 Q5AAJ7.1 B8N4P0.1 Q4WD56.1Q4WPP2.1 Q4WPM6.1 P53704.1 P0CU37.1 Q5APK7.1 Q5A8H7.1 B8NPN0.1 Q4WIN6.1Q4WWQ6.1 Q4WWW3.1 Q59VR1.1 Q5AF95.1 Q59ST1.1 Q59U81.1 B8NQ08.1 Q4U3E8.1Q4WNI0.1 Q4WSI0.1 G1UB67.1 Q59MW2.1 Q5A7N3.1 Q5APB6.1 B8N3N5.1 Q4X195.1Q4WDG1.1 Q4WNY4.1 P52496.1 Q59550.1 Q5ANP2.1 Q59WD5.1 Q00049.1 P0C955.1Q4X0Z7.1 Q4WVF4.1 Q9HEW1.1 Q5AD78.1 O59933.1 Q5ABA2.1 B8NDP1.1 Q4WRH9.1Q4WMS3.1 Q4WP02.1 Q5A6B6.1 Q5AMM4.1 Q3MPQ4.1 Q5A861.1 B8NEM4.1 Q4WVD1.1Q4WN42.1 Q4WWH6.1 Q5A1W9.1 Q5AAW3.1 Q59MP1.1 Q5AH87.1 Q9P8Z9.1 Q4WID6.1Q4WJH6.1 Q4WVE5.1 P30418.1 Q59MG1.1 Q59MB6.1 P33181.1 B8MZJ8.1 Q4WFX9.1Q4WYS1.1 Q4WHP3.1 Q59SN6.1 Q5ACK7.1 Q5A216.1 Q59Q43.1 B8NX10.1 Q4WRE4.1Q4WJ01.1 Q4WRE2.1 Q5A343.1 Q5A218.1 Q9UVL1.1 Q5A860.1 B8NV05.1 Q4WC60.1Q4WGL2.1 Q4WYX0.1 Q5ABZ2.1 Q595J9.1 Q59Y57.1 Q59ZW9.1 B8NEI6.1 Q4WR18.1Q4WP49.1 Q4WRB8.1 Q59MJ1.1 Q5AD49.1 Q5AGA0.1 A0A1D8P178.1 B8MZI5.1Q4WQY6.1 Q4WPE6.1 Q4WI88.1 Q5AJ71.1 Q59NX9.1 Q5A687.1 Q59R24.1 B8NSJ0.1Q4WXK4.1 Q4WWW9.1 Q4WQL0.1 O74201.1 Q5A119.1 Q59R28.1 Q5AHJ5.1 B8NDR8.1Q4WI96.1 Q4WKB5.1 Q4WDZ0.1 Q5AK54.1 Q59K07.1 Q5AJS6.1 P0C0X3.1 B8NDQ2.1Q4WVH4.1 Q4WA38.1 Q4WA70.1 O93852.1 Q5AKA5.1 Q5AD59.1 Q59KL6.1 B8N9M0.1A4D9R2.1 Q4WHL1.1 Q4WQ82.1 Q5AIR7.1 Q59QC2.1 Q5AG73.1 P43072.1 B8NLN6.1P0C956.1 Q4X1X0.1 Q4WMX7.1 Q5A8K2.1 Q5AL45.1 Q5AND1.1 Q5AF54.1 B8N9X2.1Q4WR22.1 Q4WRX2.1 Q4X0V2.1 Q8TGB2.1 P0CY19.1 Q59NG5.1 Q59W44.1 B8NM08.1Q4WQY8.1 Q4WDH9.1 Q4WI16.1 Q5A477.1 Q5AGC4.1 Q59N20.1 P48990.1 B8NSD4.1Q4WJJ3.1 Q4WMG1.1 Q4WXA1.1 Q5AP95.1 Q5ALP1.1 Q59WJ5.1 Q59U67.1 B8N122.1Q4X265.1 Q4WDE0.1 Q4WCV5.1 Q5AF03.1 Q5AK42.1 Q5AA50.1 Q5ANB7.1 B8NCF0.1Q9UVX3.1 Q4WCX4.1 Q4W9M7.1 Q5AMQ4.1 Q5APG7.1 Q5A319.1 Q5A3Y5.1 B8NKS1.1Q4WR19.1 Q4X122.1 Q4WQY9.1 Q5ANI6.1 Q59Y20.1 Q5AD27.1 Q59512.1 B8N3R8.1Q4WTF3.1 Q4WZF1.1 Q4WX30.1 P78595.1 Q5ALL3.1 Q5AHI7.1 Q5APA2.1 B8NG55.1Q4WLY1.1 Q4WMU1.1 Q4WUT7.1 Q87414.1 Q5AAT0.1 Q5ANE3.1 P12461.1 B8N0Q7.1Q4WMU3.1 Q4WGB7.1 Q4WIQ2.1 Q9UWF6.1 Q59QD6.1 Q59506.1 Q59TN1.1 B8N513.1Q4WQG5.1 A4DA73.1 Q4X022.1 Q9UW12.1 Q5AML1.1 P87185.1 Q5A416.1 B8N4F5.1Q4WPE9.1 Q4WD81.1 Q4WQZ0.1 Q5AAL9.1 Q5ACM9.1 Q5AM50.1 043133.1 B8NT06.1Q4WAZ4.1 Q4WHG0.1 Q4WE58.1 Q5AD56.1 Q59Z14.1 Q9B8C8.1 Q59MI8.1 B8NHF2.1Q4WLN7.1 Q4WAJ6.1 Q4WJR4.1 Q5A757.1 Q5AAG1.1 Q9B8C9.1 Q5A302.1 B8MWR8.1Q4WRB0.1 Q4WCL1.1 Q4WQZ1.1 P28870.1 Q59YL9.1 Q9B8D2.1 Q5AH60.1 B8N4G0.1Q4WC55.1 Q9HEQ8.1 Q4WQY7.1 Q59NX5.1 Q59PL9.1 Q9B8D1.1 Q5A692.1 B8N9M5.1Q4WMV5.1 Q4WEN1.1 Q4WQY5.1 Q5ABG1.1 Q59QL0.1 Q59M69.1 Q59Q39.1 Q00278.1Q4WAZ2.1 Q4WI37.1 Q4WXT2.1 Q5AP52.1 Q5A1U8.1 Q59VX9.1 Q59NW5.1 B8NPX1.1Q92197.1 Q4WZ51.1 Q8J130.1 P0CY31.1 O74198.1 Q59YD8.1 Q5A6Q4.1 B8NYW8.1Q4WSE8.1 Q4WDA4.1 Q4WJX5.1 P13649.1 Q5A013.1 Q59QH0.1 P43075.1 B8N219.1Q4WX94.1 Q4WLS7.1 Q4X1I8.1 Q5AG77.1 P87163.1 Q5A8A2.1 Q59Q36.1 B8NQK0.1Q4WLD0.1 Q4WWM6.1 Q4WVW4.1 Q9UW13.1 Q5AI86.1 Q9B8D7.1 Q92410.1 Q12732.1Q4WUK5.1 Q4WP81.1 Q4WTH1.1 P0CU34.1 Q5AM80.1 Q9UW25.1 Q5A1M4.1 Q9HEY7.1Q8TGG5.1 Q6MYT0.1 Q4WLI9.1 P40954.1 Q5A6Q7.1 Q59XY9.1 Q5ANC8.1 Q6UEG8.1Q4WTK9.1 Q4WTL0.1 Q4WQJ5.1 Q04802.1 Q5AGV4.1 Q5A2T0.1 Q5A4K7.1 O42716.1Q4WVU5.1 Q4WXV2.1 Q4WQJ2.1 P0CY35.1 Q5AJ82.1 Q5AGW8.1 Q5ADL8.1 Q9UW95.1Q4WLM7.1 Q4X0Z3.1 Q4WK56.1 Q5AAU5.1 Q5AIA1.1 Q5ADS3.1 Q59RQ2.1 Q9Y8D9.1Q4W9P4.1 Q4WN25.1 Q4WJS2.1 Q59VQ8.1 Q5A9Z6.1 Q5ACR4.1 Q5APC0.1 A2SZW8.1Q4WIT0.1 Q4WN21.1 Q4WJT9.1 Q59VF4.1 Q5AGC1.1 P0CU36.1 Q5A931.1 Q2U2U3.1Q4WQB9.1 Q4X1N0.1 Q4WUV8.1 Q5A0X8.1 Q59ZV5.1 Q5A2Y7.1 Q59VW7.1 Q00258.1Q4WGK6.1 Q4WQV2.1 Q4WX68.1 O13426.1 Q59VP7.1 Q5A368.1 Q5AKU5.1 Q12437.1Q4WMR0.1 Q4WZP2.1 Q4WHN8.1 Q5A0M4.1 Q5A7P3.1 Q9B8D6.1 Q59MN0.1 E9QYP0.1Q4WYE5.1 Q4WVK2.1 Q4WJU8.1 Q59PF9.1 Q5A6K8.1 Q9B8D0.1 Q59WH7.1 Q4WS76.1Q4WZ01.1 Q4WUA0.1 Q4WBT4.1 Q5AFP3.1 Q5AD13.1 Q5A2K0.1 Q96WL3.1 Q4WMJ7.1Q4W930.1 A4DA84.1 Q4WZV6.1 Q5AEK8.1 Q04782.1 Q5A1Q5.1 Q59ZX6.1 P28296.1Q4WBR0.1 Q4WJX0.1 Q4WUV9.1 Q5AFK0.1 Q5A0J9.1 Q5AEM5.1 Q59MU1.1 E9RAH5.1Q4WHD1.1 Q4WP38.1 Q4WLV2.1 Q5APD4.1 Q59ZZ6.1 Q5AK25.1 Q5A0J0.1 Q4WW81.1Q4WTB3.1 Q4X1D7.1 Q4WFS2.1 Q5ADQ9.1 Q5AH25.1 Q5AK10.1 Q59WK2.1 Q50EL0.1Q4WRV9.1 Q4W9Z9.1 Q4WBM1.1 P83779.1 Q59XM1.1 Q5AI15.1 P43073.1 Q4WY82.1Q4X267.1 Q4WE62.1 Q4WAU7.1 Q5AAH2.1 Q59NN8.1 Q5AEM8.1 P87220.1 Q4WSF6.1Q4WVZ3.1 Q4WZL3.1 Q4WZS3.1 O74254.1 Q5AP65.1 Q5A4J4.1 Q5ABD9.1 E9RCK4.1Q4WR24.1 Q4WB37.1 Q4WPU9.1 Q5AL49.1 Q5AFF7.1 Q59YK4.1 P83781.1 Q4WZA8.1Q4WPM8.1 Q4W9Z4.1 Q4WVZ0.1 P53697.1 Q59VR3.1 Q59WV0.1 Q5ANB1.1 Q4WAW7.1Q4WE86.1 Q4WDD0.1 Q4WCX9.1 Q5ACL7.1 Q5AFH3.1 Q5ABB1.1 Q5A0E2.1 Q92405.1A4DA70.1 Q4WKB9.1 Q4WJ38.1 Q5AEM6.1 P83780.1 Q5APK0.1 Q5AMG5.1 Q4WRY5.1Q4WW45.1 Q4WU07.1 Q4WRC2.1 Q8TG40.1 Q5A4G9.1 Q59PW0.1 Q5A6T8.1 Q7Z7W6.1Q4WVG2.1 Q4WBL6.1 Q4WWW5.1 Q59X38.1 Q59NQ9.1 O74711.1 Q59WG5.1 Q4WZ67.1Q4WQG9.1 Q4WX13.1 Q4WC84.1 Q59VQ3.1 A0A1D8PNP3.1 Q5ADN9.1 Q5AI80.1Q4WZB3.1 Q4WQN1.1 Q4WV71.1 Q4WTW3.1 Q5A7Q2.1 Q5A9Z1.1 Q5ACP5.1 Q5AB49.1Q4WLN1.1 Q4WCF1.1 Q4X0C2.1 Q4WFV6.1 Q5AJV5.1 A0A1D8PK89.1 Q5A1E1.1Q59R32.1 Q4WR82.1 Q4WZC3.1 Q4WRU4.1 Q4WKD9.1 Q5A3Z6.1 Q59WB3.1 Q59L86.1Q5A061.1 O14434.1 Q4WYX7.1 Q4WGS4.1 Q4WP10.1 Q5A201.1 Q59ZC8.1 Q5AD23.1Q59P50.1 Q4WMK0.1 Q4X0A5.1 Q4WP13.1 C5JZM2.1 O93827.1 Q5A1L6.1 Q5A5U6.1Q59WC6.1 Q4WPX2.1 Q4WUD3.1 Q4WHG5.1 P0DJ06.1 Q5AAI8.1 A0A1D8PN14.1Q5ADQ7.1 Q5AI48.1 O43099.1 Q4WS49.1 Q4WPF7.1 P46598.1 Q5A2J7.1 Q5A8X7.1Q59WJ4.1 Q59ZU1.1 Q4WJ81.1 Q4WCX7.1 Q4WH83.1 P87020.1 P22011.1 Q59X39.1Q5AGV7.1 Q5AG56.1 P67875.1 Q4WXX5.1 Q4WXW1.1 P38110.1 Q9HGT6.1 Q5ACW6.1Q59NR8.1 Q59T36.1 Q4WZB4.1 Q4WNB5.1 Q8NJM2.1 C1GK29.1 Q9UW26.1 P0CB54.1Q5A5K7.1 Q9P840.1 E9QUT3.1 O42799.1 Q4WWD3.1 Q59LX5.1 A0A1D8PN88.1Q5A210.1 Q5ABB8.1 Q4WAZ9.1 Q4WHA3.1 Q4WPU8.1 Q59PT0.1 A0A1D8PMB1.1Q59N10.1 Q5AKU3.1 Q4WZ70.1 Q4W9M3.1 Q4WN99.1 Q3MNT0.1 Q5ABR2.1 Q5A1B3.1Q59ZW4.1 E9RBR0.1 Q4WVH5.1 P0C959.1

TABLE 6 LIST OF ACCESSION NUMBERS FOR ALLERGENS FROM IEDB &ALLERGENONLINE P19594.1 P28335.1 P29000.1 M5ECN9.1 P38948.1 P00709.1P79085.1 P49148.1 Q6R4B4.1 P42037.1 Q9HDT3.1 P42058.1 P0C0Y4.1 P27759.1Q2KN25.1 P00304.1 Q2KN24.1 Q2KN27.1 P43174.1 P10414.1 Q8L5L5.1 Q8GZP6.1Q8H2B8.1 Q7Z1K3.1 A1IKL2.1 Q7M1X6.1 P49372.1 P00630.1 P43238.1 Q45W87.1Q6PSU2.1 O82580.1 Q647G9.1 Q9SQH1.1 C7E3T4.1 H6VGI3.1 Q84ZX5.1 A0PJ16.1P67875.1 P40292.1 P28296.1 P79017.1 Q96X30.1 Q4WWX5.1 O60024.1 Q92450.1Q09072.1 Q09097.1 P04403.1 P15494.1 P25816.1 P43187.1 Q39419.1 O65002.1P05814.1 P13916.1 Q9UAM5.1 P54958.1 D0VNY7.1 P54962.1 O18598.1 Q1A7B3.1Q9NG56.1 A0ERA8.1 Q8MUF6.1 A7IZE9.1 O96870.1 P02663.1 P02666.1 P02668.1Q28133.1 P00711.1 P02754.1 P02769.1 P02662.1 O18873.1 P49822.1 P09582.1B5KVH4.1 Q14790.1 E9R5X9.1 Q96385.1 Q7M1E7.1 P02229.1 Q7XCK6.1 P40108.1P42039.1 P42040.1 P42059.1 P0C0Y5.1 P02465.1 Q6IQX2.1 P20023.1 Q08407.1Q8S4P9.1 Q9ATH2.1 Q8W1C2.1 P18632.1 P43212.1 Q9SCG9.1 Q9M4S6.1 Q69CS2.1Q96VP3.1 O04701.1 O04725.1 P94092.1 P04800.1 Q7M1X8.1 Q41183.1 P93124.1P82946.1 O04298.1 Q58A71.1 Q23939.1 Q967Z0.1 Q1M2P5.1 Q94507.1 Q8MVU3.1Q86R84.1 Q00855.1 P49275.1 Q26456.1 P08176.1 Q8N0N0.1 P49278.1 Q2L7C5.1P39675.1 Q9Y197.1 P14004.1 P49273.1 Q7Z163.1 Q9UL01.1 O15315.1 P11388.1P30575.1 Q95182.1 P41091.1 O15371.1 P25780.1 Q2PS07.1 P49327.1 P30438.1Q5VFH6.1 Q7XAV4.1 P04075.1 Q90YL0.1 P01005.1 P01012.1 P19121.1 P02230.1P02224.1 P02227.1 Q9NJQ6.1 O65809.1 P26987.1 P04776.1 P04347.1 P04405.1P08238.1 P12031.1 P15252.1 Q7Y1X1.1 P52407.1 O82803.1 Q39967.1 P02877.1P62805.1 P43216.1 O23972.1 P24337.1 Q7Y1C1.1 P93198.1 Q9SEW4.1 Q2TPW5.1P81294.1 P81295.1 O64943.1 P07498.1 Q84UI1.1 P80384.1 P31025.1 Q004B5.1P14946.1 Q7M1X5.1 P14947.1 P14948.1 Q5TIW3.1 Q40237.1 P14174.1 Q5H786.1P30440.1 P11589.1 P43211.1 P40967.1 Q01726.1 Q16655.1 Q07932.1 Q9ZNZ4.1Q9H009.1 P12036.1 Q15233.1 Q5RZZ3.1 Q8GZB0.1 Q8NFH4.1 P19963.1 Q94G86.1P01014.1 P22895.1 P43217.1 P55958.1 B8PYF3.1 O75475.1 O24554.1 Q0IX90.1Q52PJ2.1 K7VAC2.1 Q3Y8M6.1 Q9URR2.1 Q9P8G3.1 A1KYZ2.1 P23284.1 Q9TZR6.1Q25641.1 P00433.1 Q41260.1 P56164.1 Q40967.1 Q8H6L7.1 P35079.1 Q9XG86.1P43214.1 Q5ZQK5.1 Q40960.1 P43215.1 O82040.1 Q8L5D8.1 P82242.1 Q9HCM2.1Q9ZP03.1 Q9FPR0.1 B6T2Z8.1 Q9C5M8.1 P15722.1 P25788.1 P81651.1 O24248.1P82534.1 E3SH28.1 O65457.1 B6RQS1.1 P02761.1 P67876.1 Q9Y4W2.1 Q9ULX3.1P83181.1 Q8L5K9.1 C1KEU0.1 Q91482.1 Q9XHP1.1 P15322.1 Q15020.1 B9SA35.1P01267.1 O00267.1 D2T2K3.1 Q9T0P1.1 Q07283.1 Q7M3Y8.1 P25445.1 Q5NT95.1P07101.1 O15205.1 O00762.1 D2KFG9.1 H9AXB3.1 Q8W3V4.1 P49370.1 Q05110.1Q9ULJ6.1 Q2VST0.1 ABL09307.1 ABL09312.1 AGC39172.1 AGC39173.1 AGC39174.1P00785.4 P85204.1 AGC39168.1 CAM31908.1 ABB77213.1 P83958.1 AGC39176.1CAA34486.1 AAA32629.1 A5HII1.1 CAM31909.1 P85206.1 P86137.2 P85524.1CAI38795.2 ABQ42566.1 AAR92223.1 P84527.1 AGC39164.1 AGC39165.1AGC39166.1 AGC39167.1 4X9U_B AGC39169.1 AGC39170.1 AGC39171.1 AAC37218.1P50635.2 XP_001657556.2 P18153.2 AAB58417.1 ABF18122.1 XP_001653462.1XP_001654143.1 XP_001654291.1 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ABU97466.1AAM83103.1 AAA78904.1 2MFK_A AAC80579.1 ABH06350.1 ABH06347.1 ABH06346.1ABH06348.1 AAX34047.1 AAM10779.1 AAQ24542.1 AAQ24543.1 AAD10850.1ABH06352.1 ABH06359.1 2JMH_A APU87558.1 APU87557.1 APU87556.1 APU87554.1AAQ24545.1 ASX95438.1 AAP35069.1 ACV04860.1 Q7M4I6.1 Q7M4I3.1 P82971.1P0CH88.1 ABB88514.1 XP_005902099.2 AAA62707.1 AAA30429.1 AAA30478.1NP_851372.1 ABW98943.1 ABW98945.1 ABW98953.1 NP_776953.1 AAA30430.1AAA30431.1 AAB29137.1 AAA30433.1 NP_776719.1 Q28133.1 Q28050.1CAA29664.1 AAA30615.1 CAA32835.1 AAA30413.1 P02754.3 ACG59280.1AAA51411.1 CAA76847.1 NP_776945.1 NP_851341.1 P80207.1 P80208.1 S65144S65145 AAN86249.1 XP_013623213.1 S65143 CAA46782.1 BAA09634.1 P69199.1P81729.1 CAA57342.1 AAN11300.1 P30575.1 AAC48794.1 CAD82911.1 CAD82912.1AAC48795.1 AAB30434.1 CAA76841.1 BAC10663.1 ACY38525.1 AHY24648.1CAA68720.1 CCF72371.1 CCK33472.1 CAC34055.2 CAD10376.1 AAB02650.1CAA47357.1 CAB02206.1 CAB02207.1 CAB02208.1 CAB02215.1 CAB02216.1CAB02217.1 AAB20453.1 ABZ81044.1 ABZ81040.1 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ACR43477.1ACR43478.1 ACR43476.1 BAH10152.1 ARX70262.1 AAC61869.1 AAW81034.1BAD77932.1 BAA05543.1 BAA05542.1 BAA07020.1 P43212.1 BAC23082.1BAC23083.1 BAC23084.1 BAF32105.1 BAF32110.1 BAF32116.1 BAF32119.1BAF32122.1 BAF32128.1 BAF32130.1 BAF32133.1 BAF32134.1 BAA06172.1BAF45320.1 AAK27264.1 BA194503.1 BAJ04354.1 BAF51970.1 BAA06905.1CAD92666.1 AAW69549.1 P83834.1 ACB45874.1 AAP13533.2 CAB62551.1CAC37790.2 ABK78766.1 ACY01951.1 CAC05258.1 AAF72625.1 AAF72626.1AAF72627.1 AAF72628.1 AAF72629.1 AAR21074.1 AAR21073.1 AAB28566.1AAB28567.1 AAB32317.1 AAF80379.2 AAK96255.1 AAL14077.1 AAL14078.1AAL14079.1 AAB50734.2 CAA69670.1 CAA01909.1 CAA01910.1 CAA62634.1AAS02108.1 CAC83658.1 CAC83659.1 CAD20406.1 AAP96759.1 2103117ACAA10345.1 AAB42200.1 P82946.1 AAK62278.1 CAD20405.1 AEY79726.1AAB01092.1 BAA13604.1 CAB03715.1 CAB03716.1 CAB06416.1 AAL76932.1BAB88129.1 ADL32660.1 ADL32661.1 ADL32662.1 ADL32663.1 ADL32664.1ADL32665.1 ADL32666.1 AAL76933.1 AEY79728.1 AEY79727.1 CAA55072.2CAA55067.2 CAA55070.1 P42040.2 CAA55068.1 AAO91801.1 AAX14379.1 P40918.1CAD42710.1 ABA42918.1 CAD38166.1 AT108931.1 L7UZ85.1 AAP35078.1AAD52672.1 AAM64112.1 AAP57094.1 ABU97470.1 AIO08850.1 AGI78542.1AGC56216.1 AIO08860.1 AAP35082.1 AIO08851.1 AGC56218.1 AIO08848.1AAP35065.1 AGC56219.1 AIO08870.1 AIO08861.1 BAX34757.1 BAE45865.1AAP35068.1 ABO84970.1 ABO84971.1 ABO84972.1 ABO84973.1 P16311.2BAC53948.1 ABA39436.1 ABU49605.1 AAP35075.1 AFJ68066.1 ADM52184.1ABL84749.1 ABL84750.1 ABL84751.1 BAA04557.1 AAK39511.1 AIO08864.1P39673.1 BAA04558.1 BAA01240.1 BAA01241.1 AAL47677.1 CAI05850.1CAI05849.1 CAI05848.1 ABA39438.1 BAD74060.2 AAP35073.1 AFJ68072.1BAA01239.1 ABN14313.1 AAA99805.1 ABY28115.1 ACK76291.1 ACK76292.1BAA09920.1 AAB27594.1 ACK76296.1 ACK76297.1 AAF28423.1 AAP35077.1ACK76299.1 AIO08853.1 AAM19082.1 AB084963.1 AB084964.1 ABO84966.1ABO84967.1 ABO84968.1 ABO84969.1 AHC94806.1 BAV90601.1 AHX03180.1AIP86946.1 AIP86945.1 AIP86944.1 AIP86943.1 AIP86942.1 AIP86941.1AIP86940.1 AIP86939.1 AJF93907.1 AAP35080.1 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AAC82351.1 AAC82352.1 AAC82350.1AAC82349.1 BAK09233.1 BAK09232.1 BAB79444.1 BAO50872.1 BAO50870.1AAX57578.1 ABC18306.1 O23878.1 O23880.1 Q9XFM4.1 ABQ10638.1 BAT21117.1ABO93594.1 ADW27428.1 ABI32184.1 ACJ23865.1 ACJ23864.1 ACJ23866.1AAZ76743.1 CAA44343.1 CAA44344.1 P30438.2 AAC37318.1 NP_001041618.1CAA44345.1 AAC41616.1 CAA59279.1 AAL49391.1 AAS77253.1 ADK56160.1ADM15668.1 AAS98889.1 AAS98890.1 AGT20779.1 AEM89226.1 ACD65080.1ACD65081.1 CAJ85646.1 CAJ85644.1 CAJ85642.1 CAJ85641.1 ABD39049.1ACX47057.1 ACX47058.1 4C9C_B CAC86258.1 AAY83342.1 AAY83341.1 AAY83345.1AHL24661.1 AHL24660.1 AAQ83588.1 AAV74343.1 AAQ08947.1 BAH10153.1AAN73248.1 AAL79930.1 AAL79931.1 AHY02994.1 P02622.1 AAK63086.1AAK63087.1 CAM56785.1 CAM56786.1 B3A0L6.1 P86980.1 NP_990450.1 P01005.1ACJ04729.1 CAA23681.1 P01012.2 CAA23682.1 1JTI_A 1UHG_D CAA26040.1P02789.2 P00698.1 AAA48944.1 CAA23711.1 CAA43098.1 BAA13973.1 P02604.3CAX32963.1 ADD18879.1 ADD19985.1 ADD19989.1 AAF82096.1 ACS49840.1P24337.1 CAA11755.1 ABU97472.1 CAA11756.1 CAA42646.1 CAA35691.1AAA33947.1 BAA23360.2 AAB01374.1 BAB64303.1 BAA74452.2 BAB64306.1P25974.1 CAA26723.1 AAA33966.1 CAA26575.1 BAA00154.1 CAA33217.1CAA37044.1 CAA26478.1 BAA74953.1 AAA33964.1 AAA33965.1 BAB15802.1AAD09630.1 NP_001238443.1 ACD36976.1 ACD36975.1 ACD36974.1 ACD36978.1BAB21619.2 P22895.1 AAB09252.1 BAA25899.1 P82947.1 CAA45777.1 CAA45778.1AAB23464.1 AAB23482.1 AAB23483.1 CAA56343.1 CAA60533.1 CAB59976.1CAB76459.1 AAQ54603.1 BAH10148.1 BAJ61596.1 AAG08987.1 APG42675.1CAA75506.1 AAP47226.1 P23110.1 CAB38044.1 CAA39880.1 AAA16792.1CAB53458.1 CAC13961.1 CAC42881.1 AAL25839.1 AAP37470.1 ADR82196.1CCW27997.1 AAA87456.1 AAP87281.1 ABN03965.1 ABN03966.1 ABN09653.1ABN09654.1 ABN09655.1 ACY91851.1 ACZ74626.1 AEV41413.1 AFJ97275.1AFJ97274.1 AAC82355.1 AAR98518.1 AAC49447.1 CAA05978.1 1WKX_A ABW34946.1AAC27724.1 CAA11041.1 CAA11042.1 AAF25553.1 CAE85467.1 CAA75312.1 1G5U_AAAF34341.1 AAF34342.1 AAF34343.1 CAB51914.1 CAB96215.1 CAC00532.1Q9LEI9.1 CAD24068.1 CAA81610.1 CAA93121.1 CAA10140.1 Q7M262 CAB10766.1CAB10765.1 AAG42255.1 AAC48288.1 AAC48287.1 P32936.2 P80198.1 CAA51204.1CAA42832.1 AAA32970.1 CAA35188.1 CAA08836.1 CAA41956.1 CAA49555.1CAA45085.1 CAA46705.1 AAP94213.1 AAP15200.1 AAP15199.1 AAM54365.1AAM54366.1 APR62629.1 AAB41308.1 AAF18269.1 ACI47547.1 AAW29810.1CAC05582.1 P81295.1 AAD03608.1 CAC48400.1 AAC15474.2 AAR21072.1AAR21071.1 Q9LD79.2 AAF80164.1 AAF80166.1 AAV97933.1 AAT45383.1AAX35807.1 CAD87730.1 CAD87731.1 AAQ55550.1 CAB71342.1 CAB62213.1CAD32313.1 CAD32314.1 2118249B 2118249A AAQ73484.1 AAQ73486.1 AAQ73487.1AAQ73488.1 AAQ73489.1 AAQ73490.1 AAQ73491.1 AAQ73492.1 CAA57160.1CAA58755.1 AAQ73493.1 AAQ73494.1 CAB62212.1 CAB65963.1 CAP17694.1CAC84590.2 CAC84593.2 CAA54818.1 CAA54819.1 AAZ91659.1 BAW03243.1BAW03242.1 AAL07320.1 ABC02750.1 ACM89179.1 ACB38288.1 ABI98020.1ACC76803.1 P14946.2 AAA63278.1 AAA63279.1 CAB63699.1 Q7M1X5.1 P14947.1CAA51775.1 P14948.1 CAH92637.1 AAD20386.1 CAB64344.1 AAA33405.1 Q40240.2CAI84850.2 Q53HY0.2 Q6EBC1.1 ABR21771.1 ABR21772.1 ACB05815.1 F5B8W5.1F5B8W4.1 F5B8W3.1 F5B8W2.1 F5B8W1.1 F5B8W0.1 F5B8V9.1 B3A0N2.1ADC55380.1 AHA85706.1 P86739.1 P86741.1 P86740.1 P86742.1 BAA32435.1BAA32436.1 AAD25927.1 CAA65341.1 CAD20981.3 CAD68071.1 CAI43283.4CAA09883.1 CAA09884.1 CAA09885.1 CAA09886.2 CAA09887.4 CCU97864.1CCV00099.1 CCU98198.1 CCU99457.1 SHO79205.1 CCU99206.1 CAA96534.1CAA96535.1 CAA96536.1 CAA96537.1 AAD13683.1 AAD26546.1 AAD26547.1AAD26548.1 AAD26552.1 AAD26553.1 AAD26554.1 AAD26555.1 AAD26558.1CAD32318.1 AAO25113.1 AAD29671.1 AAB01362.1 CAA88833.1 CAA58646.1AAK13029.1 AAK13030.1 AAK13027.1 AAB35897.1 AAX19848.1 AAX19851.1Q9FSG7.1 CAT99612.1 CAT99611.1 AFM77001.1 AAC36740.1 O29330.1 AAT80665.1AAT80664.1 AAT80662.1 AAT80659.1 AAT80649.1 AAR22488.1 Q9M5X7.1CAD46559.1 CAD46561.1 CAD46560.1 AAX19854.1 AAX19856.1 AAX19858.1AAX19860.1 CAK93713.1 CAK93753.1 CAK93757.1 CAT99618.1 CAT99619.1CAT99617.1 AAD29412.1 AAD29413.1 AAD29414.1 AAM55492.1 AEE98392.1B3EWS0.1 B3EWE5.3 G5DC91.2 BAF47263.1 AGF86397.1 CAA73720.1 P86745.1P86749.1 P86750.1 P86752.1 P86753.1 P86754.1 P86757.1 P86761.1 P86760.1P02620.1 P86765.1 P86768.1 P86769.1 P86770.1 P86771.1 P86772.1 P86774.1P86775.1 AAD55792.2 Q99MG7.1 AAA60330.1 AAG08989.1 AHW81906.1 AAV33670.1AAV33672.1 P85894.1 P02762.2 CAA26953.1 A2BIM8.1 AAA39768.1 AAK54834.12CYG_A 1Z3Q_A CAC81811.1 AAB82772.2 BAD36780.1 AAB50883.1 CAA49760.12206305A AAB36316.1 BAH10150.1 CAE17317.1 CAE17316.1 BAE54433.1 P19963.2I53806 E53806 F53806 C53806 A38968 G53806 B53806 H53806 CAA73038.1CAA73037.1 CAA73036.1 AAB32652.2 AAO22133.1 AAO22132.1 AAN18044.1AAQ10281.1 AAQ10280.1 AAQ10279.1 AAQ10278.1 AAQ10277.1 AAQ10276.1AAQ10274.1 AAQ10271.1 AAQ10268.1 AAQ08190.1 ABP58632.1 ABP58633.1ABP58635.1 ABP58636.1 ABP58637.1 AAL92578.1 AAY88919.1 ACZ57582.1E1U332.1 E3SU11.1 O24170.1 O24171.1 A4GFC0.1 A4GFC3.1 CAA73035.1AAD05375.1 AAO33897.1 P80740.2 CAD21706.2 ABP58627.1 ABX26131.1ABX26132.1 ABX26134.1 ABX26138.1 ABX26139.1 ABX26140.1 ABX26141.1ABX26143.1 ABX26145.1 ABX26147.1 ABX54842.1 ABX54844.1 ABX54849.1ABX54855.1 ABX54859.1 ABX54862.1 ABX54864.1 ABX54866.1 ABX54869.1ABX54876.1 ABX54877.1 AAB66909.1 P81430.2 AAF31152.1 AAF31151.1AAK58515.1 2JON_A BAE54432.1 Q25632.1 BAJ07603.1 P86431.1 P86432.1BAF95206.1 AFV53352.1 AAG42806.1 AAG42802.1 Q948T6.2 AAA86533.1AAF72991.1 BAB71741.1 Q40638.2 BAD13150.1 BAC20657.1 BAA01998.1BAA01996.1 BAA07772.1 BAA07773.1 BAA07774.1 BAA07710.1 BAA07711.1BAA07712.1 BAA07713.1 AAB99797.1 Q01882.2 Q01883.2 BAC19997.1 BAC20650.1ADK39021.1 ACA96507.1 CBY17558.1 AAC38996.1 BAF47265.1 BAF47266.12008179A CAA65123.1 CAA54587.1 CAI94601.1 CAA59370.1 CAA65122.1 P55958.1Q9T0M8.1 Q9XG85.1 CCP19647.1 CAP05019.1 Q7M1E8 AAB36008.1 AAB36009.1AAB36010.1 AAB36011.1 AAB36012.1 AAB46820.1 AAB46819.1 AKF12278.1CBM42667.1 CBM42666.1 CBM42665.1 CBM42664.1 CBM42663.1 CBM42662.1CBM42661.1 CBM42660.1 ACA23876.1 AAX37288.1 AAO15713.1 C7E3T4.1ADV17342.1 ADV17343.1 AAX11194.1 AAF71379.1 AAG44693.2 AAF23726.1AAM33821.1 AAB34785.1 ADK27483.1 AAD25995.1 AAG44480.1 Q92260.1AAK51201.1 AAR17475.1 AAD42074.1 ABB89950.1 ABM60783.1 AAD25926.1AEX34122.1 AAG44478.1 AKH04310.1 AKH04311.1 AAX33729.1 AEV23867.1AAD19606.1 CAB38086.1 ACS14052.1 AAC34736.1 AAC34737.1 AAB82404.1AAC34312.1 AAD13533.1 AAP13554.1 ADB92492.1 AAX33734.1 AAX33727.1ADR82198.1 AAB09632.1 AAB62731.1 AAB63595.1 Q25641.1 ADB92493.1ADD17628.1 AAX33728.1 3EBW_A ACJ37391.1 AAX33730.1 AAT77152.1 ACA00204.1AAL86701.1 AAG08988.1 CAB01591.1 AAB27445.1 Q41260.1 P56164.1 P56165.1P56166.1 P56167.1 ADC80502.1 ADC80503.1 CAA55390.1 CAA81613.1 1N10_ACAG24374.1 2118271A AAN32987.1 CAA70609.1 ABG81289.1 ABG81290.1ABG81291.1 ABG81292.1 ABG81293.1 ABG81294.1 ABG81295.1 CAA70608.1CAA54686.1 CAB42886.1 CAA53529.1 CAD54670.2 CAF32567.2 CAF32566.2CAQ55938.1 CAQ55939.1 CAQ55940.1 CAQ55941.1 3TSH_A CAD54671.2 CAA52753.1S32101 S38584 Q7M1L8 2023228A CAB05371.1 CAB05372.1 CAA50281.1AAC16525.1 AAC16526.1 AAC16527.1 AAC16528.1 AAC25994.1 AAC25995.1AAC25997.1 AAC25998.1 AAK25823.1 CAD38384.1 CAD38385.1 CAD38386.1CAD38387.1 CAD38388.1 CAD38389.1 CAD38390.1 CAD38391.1 CAD38392.1CAD38393.1 CAD38394.1 CAD38395.1 CAD38396.1 CAD38397.1 1L3P_A CAD87529.1CAA81609.1 CCD28287.1 CAA76556.1 CAA76557.1 CAA76558.1 1NLX_N CAA76887.13FT1_A AGT28425.1 CAD10390.1 AHC94918.1 CEJ95862.1 CTQ87571.1 ABU42022.1ABG73109.1 ABG73110.1 ABG73108.1 ABO36677.1 ABR29644.1 CAF25233.1CAF25232.1 CAB82855.1 AJG44053.1 A0A158V755.1 A0A158V976.1 2N81_ACAC41633.1 CAC41634.1 CAC41635.1 CAD80019.1 ABY21305.1 ABY21306.1ALF39466.1 ALF00099.1 CAD20556.1 CAE52833.1 CAC85911.1 CBW45298.1 A60372F37396 CAA10520.1 AAG42254.1 P22284.1 P22286.1 A60373 P22285.1AAA29793.1 AAD52615.1 AAD52616.1 AAT95010.1 AAS67044.1 AAS67043.1AAS67042.1 AAS67041.1 AAP37412.1 AAT95009.1 P35780.1 P83377.1 P83542.1A2VBC4.1 ADT89774.1 ADL09135.1 P86687.1 ADD63684.1 P86686.1 Q7Z156.2P05946.1 AGE44125.1 ABL89183.1 ABS12234.1 AFA45339.1 ACN87223.1AKV72167.1 AHY24177.1 BAH59276.1 AAB97141.1 ADR66945.1 ADR66946.1ADR66947.1 ADR66948.1 AAC02632.1 AAS47037.1 AAS47036.1 AAS47035.1 1H2O_AAAF26449.1 ADR66943.1 ADR66944.1 AAD29411.1 AAB38064.1 P82534.1ACE80974.1 AAL91662.1 3EHK_A AGR27935.1 ADN39440.1 ADN39441.1 P82952.1ACE80939.1 ACE80956.1 ACE80958.1 ACE80957.1 ACE80959.1 ACE80955.1ACE80972.1 P83332.1 P83335.1 AEV57471.1 ABB78006.1 AJE61291.1 AJE61290.1P81402.1 AAV40850.1 ADR66939.1 AGW21344.1 CAD37201.1 CAD37202.1 P86888.1BAH10154.1 C0HKC0.1 AHB19227.1 AHB19226.1 AHB19225.1 AAF26451.1AET05733.1 AET05732.1 AET05730.1 O65200.1 AAD29410.1 AAC24001.1ABZ81045.1 ABZ81047.1 ABZ81046.1 CAC83046.1 CAC95152.1 CAC83047.1CAC95153.1 P02761.1 Q63213 AAA41198.1 AIS82657.1 AAP30720.1 AAT37679.1CAA38097.1 ABG54495.1 ABG54494.1 Q91483.3 ACI68103.1 CAA66403.1CBL79146.1 ACH70931.1 CBL79147.1 NP_001133181.1 AHL24657.1 ARS33724.1AAT99258.1 AAX11261.1 AAX11262.1 ACO34813.1 P83181.1 ACO34814.1ACS34771.1 AHL24658.1 ADK22841.1 ADK22842.1 CAX32966.1 CAX32967.1SHD75397.1 AAO15613.1 AAS93669.1 AAS93674.1 AAS93675.1 AAS93676.1AAO15607.1 AAX37321.1 AGM48615.1 CAQ68366.1 BAH10151.1 Q7M1Y1 C37396D37396 AAP06493.1 AAC67308.1 XP_003030591.1 BAW32538.1 BAW32537.1BAW32536.1 BAW32535.1 BAC66618.1 CAX32965.1 AFA45340.1 AFJ80778.1ABS12233.1 CAQ72968.1 CAQ72969.1 AAB37403.1 AAB37406.1 AAB34365.1CAH92630.1 CAH92627.1 Q7M263 CBG76811.1 BAE54429.1 BAE54430.1 ACB55491.1AAK15088.1 ACI41244.1 AAD42943.1 AAK15089.1 AAG23840.1 ACH85188.1AAD42942.1 AAD42944.1 AAK15087.1 CAA62909.1 CAA62910.1 CAA62911.1CAA62912.1 CAA62908.1 P15322.2 AAX77383.1 AAX77384.1 ABU95411.1ABU95412.1 ABU53681.1 NP_001306883.1 NP_001316123.1 CAD10377.1AAL29690.1 AAL75449.1 AAL75450.1 CAJ19705.1 AAB42069.1 CAA75803.1AHC08074.1 AHC08073.1 ABA81885.1 ABB16985.1 CAA31575.1 CAA27571.1CAA27588.1 AAA33819.1 P15476.2 P16348.1 P20347.3 AAB63099.1 BAA04149.1BAH10156.1 AAF65312.1 AAF65313.1 AAC97370.1 AAC97369.1 AAB36117.1AAB36119.1 AAB36120.1 AAB36121.1 AAT95008.1 P35775.1 AAB65434.1 P35776.2P35779.2 ADD74392.1 AIL01319.1 AIL01318.1 AIL01316.1 AIL01317.1AIL01320.1 AIL01321.1 ACT37324.1 1ESF_B CAJ43561.1 P34071.1 P20723.1P06886.1 AAT66567.1 ABS29033.1 AAT66566.1 AAD46493.1 AAS75831.1 P00791.3AAA30988.1 NP_001005208.1 P58171.1 S43242 S43243 S43244 ADX78255.1ADM18346.1 ADM18345.1 ADK47876.1 P86360.1 CEE03319.1 CEE03318.1AAK63089.1 AAK63088.1 CBL79145.1 P86978.1 CAX62602.1 P86979.1 BAE54431.1BAE46763.1 BAH10155.1 AAF07903.2 AAD52013.1 AAD52012.1 Q8J077.1CAD23374.1 P24296.2 CAA42453.1 ACG59281.1 AKJ77988.1 AKJ77986.1AKJ77987.1 CAI64398.1 AKJ77990.1 AKJ77985.1 CAA35238.1 CAA25593.1CAA26383.1 CAA26384.1 CAA26385.1 AAA34275.1 AAA34276.1 AAA34279.1AAA34280.1 AAA34281.1 AAA34282.1 AAA34283.1 AAA34284.1 BAA12318.1P81496.1 ACE82289.1 BAE20328.1 CAR82265.1 CAR82266.1 CAR82267.1BAN29067.1 CAI64397.1 CAI64396.1 P08819.2 P27357.1 ACE82291.1 CAA61945.2CAA61943.2 CAA61944.2 CAQ57979.1 CBA13560.1 AAA34272.1 AAA34274.1AAA34288.1 AAA34289.1 BAA11251.1 CAI78902.1 BAN29066.1 CAY54134.1CAB96931.1 CAA43331.1 CAA31396.1 CAA26847.1 CAA24934.1 CAA43361.1AAB02788.1 CAA27052.1 CAA24933.1 BAN29068.1 CAA31395.4 AAZ23584.1BAC76688.1 CAI84642.1 CAA35598.1 CAZ76052.1 CBA13559.1 CAA35597.1CAC14917.1 ACE82290.1 Q6W8Q2.1 CAA72273.1 CAB52710.1 CAZ76054.1CAA31685.1 CAA30570.1 AAA34285.1 AAA34286.1 AAA34287.1 O22116 CAA59338.1CAA59339.1 CAA59340.1 O22108 CAI79052.1 AEH31546.1 BAN29069.1 CAA65313.1ABS58503.1 P82977.2 CCK33471.1 APY24042.1 CAA34709.1 CAA39099.1CAA36063.1 CAA44473.1 AAA34290.1 AAX34057.1 AAX34058.1 AAX34059.1A0D75395.1 AOD75396.1 AOD75399.1 ABQ96644.1 ABU97479.1 AAT40866.1AAU11502.1 ABM53751.1 ABU97480.1 CAA73221.1 ACL36923.1 ABZ81991.1AGG10560.1 AAT66607.1 AAT66609.1 ACH42744.1 AAT66610.1 ACJ65836.1AGC36415.1 ACH42743.1 ACI44002.1 ABQ59259.1 ABQ59258.1 ABQ59255.1ACJ54737.1 ACH42741.1 AGC36416.1 AKV72166.1 AIV43662.1 BAH10157.1P0DMB5.1 P0DMB4.1 P0CH87.1 P35781.1 P35782.1 CBY83816.1 CBY93636.1P81657.1 P35783.1 CAJ28931.1 P35784.1 CAJ28930.1 CAL59818.1 CAL59819.1P51528.1 P35760.1 ABC73068.1 P0CH89.1 P35785.1 P35786.1 P0CH86.1P35787.1 AAB48072.1 AAA30333.1 CAB42887.1 1QNX_A P49370.1 CAI77218.12ATM_A ACA00159.1 AAX19889.1 ABG02262.1 ABW23574.1 BAA74451.1 CAA50008.1P80273.2 P80274.1 P33556.1 CAR48256.1 ABD79096.1 ABD79097.1 ABD79098.1ACX37090.1 P29022.1 2209273A AAO45607.1 AAO45608.1 AAK56124.1 2HCZ_XABD79094.1 ABD79095.1 ABF81661.1 ABF81662.1 Q1ZYQ8.2 P0C1Y5.1 AAB86960.1ABG81312.1 ABG81313.1 ABG81314.1 ABG81315.1 ABG81316.1 ABG81317.1ABG81318.1 CAA51718.1 CAA51719.1 CAA51720.1 AAG35601.1 5FEF_A AAA33493.1AAA33494.1 CAI64400.1 AAX40948.1

TABLE 7 LIST OF ACCESSION NUMBERS FOR AUTOMIMMUNE ANTIGENS FROM IEDBI7HKY1.1 Q9P0J1.1 P61604.1 Q9NUQ2.1 Q9P212.1 P16885.1 P09543.1 P17980.1Q99460.1 O00231.1 000487.1 P48556.1 Q61733.1 P82909.1 P21953.1 Q9CHK3.1Q9BYD6.1 Q9BYC9.1 Q96A35.1 Q9P0J6.1 P04035.1 Q99714.1 B2RLH8.1 P62277.1P08708.1 P62269.1 P63220.1 P62851.1 P62273.1 P62861.1 P46781.1 P08865.1P17643.1 Q9H0D6.1 F5HCM1.1 E5RK45.1 A0A0B7JKK9.1 A1JIP3.1 B2RKS6.1P0A6F5.1 P0C0Z7.1 Q49375.1 Q9Z708.1 P0A521.1 P42384.1 P0A520.1 P9WPE7.1P10809.1 P10155.1 P05388.1 P05386.1 P05387.1 P27635.1 P62906.1 P40429.1P35268.1 A8MUS3.1 P62750.1 P61353.1 P46776.1 P46779.1 P47914.1 P39023.1P62888.1 Q02878.1 P18124.1 P62917.1 P32969.1 Q6SW59.1 P08253.1 P11021.1Q969T7.1 Q76LX8.1 C6AV76.1 Q2FWL5.1 B1RDC1.1 Q2G2D8.1 P42684.1 Q8IZT6.1Q9Y4K1.1 P02709.1 P02710.1 P02711.1 P04756.1 P02708.1 P02712.1 P11230.1Q07001.1 P02715.1 Q04844.1 P07510.1 P13536.1 F1N690.1 M9YGB9.1 O43427.1P68133.1 P62736.1 P60709.1 P63261.1 Q9NQW6.1 O15144.1 Q9H981.1 Q8N3C0.1Q6VMQ6.1 Q6JQN1.1 Q5T8D3.1 P82987.1 Q6ZMM2.1 Q9NZK5.1 Q8IUX7.1 Q9NP61.1Q9UJY4.1 O43488.1 P07897.1 P16112.1 Q73ZL3.1 Q92667.1 P49588.1 C9JKR2.1F8ELD9.1 P15121.1 F5HF49.1 P05186.1 P55008.1 Q5STX8.1 P02763.1 P01009.1P35368.1 P04217.1 P25100.1 P08697.1 P18825.1 P02765.1 P01023.1 P12814.1O43707.1 P35611.1 Q9UBT7.1 P61163.1 P02489.1 P02511.1 P06733.1 P06280.1Q16352.1 Q96Q83.1 P37840.1 Q9UJX4.1 P01019.1 Q9P2G1.1 Q9H8Y5.1 Q8N6D5.1H0YKS4.1 P04083.1 P50995.1 P07355.1 P08758.1 P08133.1 Q9NQ90.1 Q03518.1P01008.1 Q10567.1 Q9BXS5.1 Q96CW1.1 O00203.1 P02647.1 P02652.1 P06727.1P04114.1 P02655.1 C9JX71.1 P05090.1 P02649.1 Q9BZR8.1 P03182.1 Q9BRQ8.1Q9ATL6.1 P47863.1 P55087.1 P55064.1 P20292.1 Q15057.1 Q96P48.1 P35869.1Q5VUY2.1 P03928.1 P25705.1 P06576.1 P56385.1 Q9DB20.1 P18859.1 Q9BZC7.1Q8WWZ7.1 Q9NUT2.1 P61221.1 P53396.1 A1JNN2.1 P0A6G7.1 Q9H2U1.1 Q14562.1O84848.1 P78508.1 Q99712.1 P17342.1 Q99856.1 Q81VW6.1 Q96GD4.1 Q8WXX7.1O15392.1 P02730.1 P98160.1 F8W034.1 P20749.1 P41182.1 Q9NYF8.1 Q6W2J9.1Q8NFU0.1 P15291.1 P07550.1 P02749.1 P61769.1 Q13425.1 Q562R1.1 P42025.1P13929.1 F0K2P6.1 O43252.1 Q13057.1 Q8IUF8.1 Q8NFC6.1 P18577.1 Q5VSJ8.1Q02161.1 P02663.1 P02769.1 Q9NWK9.1 O95415.1 Q7Z569.1 Q99728.1 Q9P287.1Q9NRL2.1 Q9UIF9.1 Q58F21.1 P25440.1 Q15059.1 O60885.1 P18892.1 Q8NCU7.1P04003.1 O75844.1 P12830.1 P33151.1 Q8NE86.1 P62158.1 P07384.1 P17655.1P20810.1 P27797.1 O94985.1 P10644.1 P31321.1 P13861.1 O70739.1 Q8QVL3.1Q8QVL6.1 Q8QVL9.1 Q91CY5.1 Q91CZ6.1 Q98Y63.1 Q99AQ9.1 Q9DTD4.1 Q9DUB7.1Q9DUC1.1 Q9JG76.1 Q9QU30.1 Q9QUB8.1 Q80AR5.1 Q80QT8.1 Q8UZK7.1 P14348.1Q9H2A9.1 P00918.1 P16870.1 075339.1 O15519.1 Q14790.1 P04040.1 P35221.1P49913.1 P07858.1 P07339.1 P25774.1 Q03135.1 Q16663.1 Q9H9A5.1 Q9Y5K6.1P09326.1 P14209.1 Q99741.1 000311.1 O75794.1 P04637.1 B2RD01.1 Q03188.1P49454.1 Q9HC77.1 Q02224.1 P00450.1 P08622.1 P35514.1 Q05980.1 P9WMJ9.1Q9H444.1 P36222.1 O00299.1 P05108.1 O15335.1 Q6UVK1.1 Q9P2D1.1 P10645.1O75390.1 O14503.1 Q00610.1 P09497.1 O75508.1 P56750.1 Q9P210.1 Q7Z460.1O75122.1 O75153.1 P10909.1 Q7Z401.1 P00451.1 P00488.1 P48444.1 P61923.1E9PP50.1 P23528.1 Q8WUD4.1 Q49A88.1 Q16204.1 P38432.1 P02452.1 P02458.1P05539.1 P02462.1 G1K238.1 Q7SIB2.1 P20908.1 Q02388.1 P27658.1 P12107.1Q99715.1 Q05707.1 P39059.1 Q9UMD9.1 P08123.1 P08572.1 Q7SIB3.1 P05997.1P12110.1 P13942.1 F1MZU6.1 Q01955.1 P12111.1 P02745.1 P02746.1 P09871.1P01024.1 P0C0L5.1 P01031.1 Q07021.1 P13671.1 P02748.1 P08603.1 Q03591.1Q6PUV4.1 W1Q7Z5.1 Q15021.1 Q15003.1 P42695.1 Q14746.1 Q9NZB2.1 Q12860.1Q02246.1 P78357.1 Q9UBW8.1 P36717.1 P02741.1 P12277.1 P06732.1 H0Y8U5.1Q13618.1 Q86VP6.1 P25024.1 P16220.1 P06493.1 P11802.1 Q00534.1 P50750.1P41002.1 P04080.1 P50238.1 P52943.1 O14957.1 P20674.1 P10606.1 P14854.1P15954.1 P10176.1 Q16678.1 P10635.1 Q14008.1 Q9Y5Y2.1 Q96KP4.1 P14416.1Q5QP82.1 P07585.1 E5RFJ0.1 Q86SQ9.1 Q9Y394.1 P49366.1 Q5QJE6.1 P24855.1Q02413.1 P32926.1 P15924.1 Q16760.1 P19572.1 A9NHS5.1 Q9JZ09.1 P06959.1P08461.1 P10515.1 P20285.1 P0AFG6.1 Q5F875.1 P19262.1 P36957.1 Q16555.1P53634.1 Q14689.1 Q13443.1 Q12959.1 Q15398.1 Q16531.1 P40692.1 P43246.1P09884.1 P03198.1 P04293.1 Q9NRF9.1 Q9UGP5.1 P89471.1 Q13426.1 P49736.1P33992.1 P11387.1 Q02880.1 Q9UBZ4.1 P24928.1 O14802.1 Q9NW08.1 P31689.1P25686.1 O60216.1 O95793.1 P55265.1 Q6P0N6.1 Q13202.1 Q8IVF4.1 E9PEB9.1Q9U114.1 P11161.1 Q14258.1 Q9ULT8.1 O95714.1 Q7Z6Z7.1 Q9Y4L5.1 O43567.1Q63HN8.1 Q969K3.1 Q8IUQ4.1 P19474.1 Q6AZZ1.1 Q9C026.1 Q14669.1 Q5T4S7.1P18146.1 Q05BV3.1 Q6ZMW3.1 O95967.1 P15502.1 Q9BY07.1 P13804.1 Q6PJG2.1A6PW80.1 P68104.1 P13639.1 Q96RP9.1 Q9BW60.1 Q9UI08.1 P17813.1 Q9NZ08.1P14625.1 Q14511.1 Q6P2E9.1 B2RLL7.1 O84591.1 Q9Z7A6.1 P03188.1 P04578.1P14075.1 Q6SW67.1 Q92817.1 P12724.1 Q12929.1 P61916.1 P07099.1 P03211.1P12978.1 P12977.1 P03203.1 P03204.1 Q99808.1 P27105.1 P03372.1 P32519.1Q15723.1 P60842.1 Q14240.1 P38919.1 P41567.1 Q14152.1 B5ME19.1 P60228.1O75821.1 Q13347.1 Q9Y262.1 F1TIN3.1 Q96KP1.1 Q96A65.1 O84646.1 Q01780.1P30822.1 O14980.1 P41180.1 P15311.1 Q08945.1 P52907.1 Q9BXW9.1 Q14296.1Q16658.1 Q7L8L6.1 Q7L5A8.1 P49327.1 Q81X29.1 Q8TB52.1 Q7Z6M2.1 Q7L513.1Q9BZ67.1 A1ZL39.1 P02792.1 P35555.1 P02671.1 P02675.1 P02679.1 Q06828.1P02751.1 Q4ZHG4.1 P20930.1 P21333.1 P30043.1 O75955.1 Q14254.1 P49771.1Q12841.1 Q13461.1 P32314.1 O95954.1 P04075.1 P09972.1 P07954.1 Q9H0Q3.1Q7Z6J4.1 P30279.1 P30281.1 O96020.1 O95067.1 P14078.1 P51570.1 Q08380.1O00214.1 Q3B8N2.1 P34903.1 P09104.1 A4D1B5.1 P17900.1 P06396.1 Q12789.1Q8WUA4.1 P03300.1 P08292.1 P27958.1 P03995.1 P14136.1 P47871.1 Q8TDQ7.1P35575.1 Q9NQR9.1 Q9Z186.1 P11413.1 P06744.1 P48318.1 Q99259.1 P48320.1Q05329.1 Q05683.1 P00367.1 Q05586.1 Q5VSF9.1 Q12879.1 S0G235.1 P15104.1Q06210.1 P35754.1 P18283.1 P09211.1 P04406.1 Q9NPB8.1 P11216.1 P06737.1P11217.1 Q31BS5.1 P04921.1 O43292.1 P30419.1 D6RB28.1 Q96S52.1 Q969N2.1Q86SQ4.1 Q9HC97.1 K7EQ05.1 P28799.1 P0A6P5.1 P44536.1 Q8WWP7.1 P62826.1P16520.1 P09471.1 Q9BVP2.1 Q9NVN8.1 P00738.1 Q9Y6N9.1 Q96CS2.1 P48723.1Q0VDF9.1 P08107.1 P34931.1 P11142.1 P04792.1 P07900.1 Q14568.1 P08238.1P54652.1 Q15477.1 P03452.1 P69905.1 P68871.1 P02042.1 P69892.1 P02790.1Q14CZ8.1 P09651.1 Q32P51.1 P14866.1 Q8WVV9.1 O43390.1 Q1KMD3.1 O88569.1P22626.1 Q9Y241.1 O95263.1 P12314.1 P09429.1 P26583.1 P25021.1 P49773.1Q9NQE9.1 P12081.1 Q9NVP2.1 Q8WU14.1 Q9H0E3.1 P07305.1 Q02539.1 P16403.1P16402.1 P10412.1 P16401.1 P0CE15.1 Q92522.1 P0C0S8.1 P0C0S9.1 Q93077.1Q9BTM1.1 Q71U19.1 P0C0S5.1 P16104.1 P62808.1 P33778.1 P62807.1 P10853.1P06899.1 O60814.1 Q99877.1 Q16778.1 Q5QNW6.1 P57053.1 P68431.1 P68432.1Q16695.1 Q71D13.1 P49450.1 P62803.1 P62805.1 P62806.1 Q99525.1 P02259.1Q9NR48.1 P01892.1 P04439.1 P16188.1 P10314.1 P01891.1 P10316.1 P13747.1P30464.1 P03989.1 P30685.1 P18463.1 Q95365.1 P30480.1 P30484.1 P30486.1P18464.1 P30490.1 P30495.1 P01889.1 Q31612.1 P30460.1 Q07000.1 Q29960.1F8W9Z8.1 Q29963.1 P10321.1 P28068.1 P20036.1 P04440.1 P01909.1 P01906.1E9PIB1.1 P01920.1 Q5Y7D6.1 P01903.1 P79483.1 P13762.1 Q30154.1 P04229.1P20039.1 Q951E3.1 Q5Y7A7.1 P01911.1 Q29974.1 P01912.1 P13760.1 Q9GZN2.1Q9H2X6.1 Q9H422.1 P51610.1 P50502.1 295441875.1 295413967.1 295413927.1295413946.1 295441907.1 295441886.1 295413949.1 312192955.1 295413970.1295413952.1 295413922.1 295413835.1 295413838.1 295413935.1 295413976.1P01880.1 Q9Y6R7.1 Q9Y5U9.1 Q5VY09.1 O14498.1 P78318.1 O00410.1 P11314.1Q9BY32.1 P01317.1 A6XGL2.1 P01308.1 F8WCM5.1 P01325.1 P01326.1 O15503.1Q13429.1 P01344.1 Q9Y287.1 O60478.1 Q8N201.1 P23229.1 Q13349.1 P08514.1P05106.1 P16144.1 Q9H008.1 Q14624.1 Q9UMF0.1 P01562.1 P01563.1 P01574.1P38484.1 P14316.1 Q15306.1 Q13568.1 P20591.1 P20592.1 Q9BYX4.1 O14879.1Q12905.1 Q12906.1 P42701.1 Q5TF58.1 Q9NZM3.1 P03956.1 Q9Y547.1 Q13099.1O60306.1 O84606.1 Q9Y283.1 P10997.1 Q05084.1 Q9P266.1 Q53G59.1 P13645.1P02533.1 P08779.1 Q04695.1 P05783.1 P35527.1 P04264.1 P35908.1 P12035.1P48668.1 P08729.1 Q07666.1 Q96EK5.1 P52732.1 Q96Q89.1 Q99661.1 P01042.1Q6NY19.1 Q13601.1 Q04760.1 P42166.1 P19137.1 P11047.1 O43813.1 P0CC04.1P23700.1 P46379.1 Q6SW84.1 P13285.1 O75845.1 P40126.1 Q99538.1 P29536.1P02750.1 Q15345.1 Q8NHL6.1 Q8NHJ6.1 Q6GTX8.1 Q9NPC1.1 Q14847.1 P61968.1P11182.1 P18428.1 P50851.1 P06858.1 P0A5J0.1 P9WK61.1 Q86W92.1 P05451.1P23141.1 P07195.1 P31994.1 P31995.1 P01130.1 Q7Z4F1.1 A4QPB2.1 P20132.1P05455.1 P18627.1 Q13094.1 P01374.1 Q8NHM5.1 O60341.1 P10253.1 O00754.1P10619.1 Q13571.1 P11279.1 Q9UQV4.1 P22897.1 P14174.1 P34810.1 Q8NDA8.1P06491.1 P07199.1 F5HDQ6.1 P03227.1 Q14764.1 P08392.1 P40925.1 P40926.1Q8N5Y2.1 Q9ULC4.1 Q961J6.1 H3BT46.1 P11226.1 Q8WXG6.1 Q92585.1 P43243.1P50281.1 P51512.1 Q9NPA2.1 P03485.1 Q96RN5.1 A6ZJ87.1 Q99705.1 P40967.1Q01726.1 Q16655.1 P15529.1 190341000.1 F5HB52.1 O00562.1 P16035.1P56192.1 Q9UBB5.1 Q29983.1 Q16891.1 P55082.1 P55083.1 P46821.1 P27816.1Q9UPY8.1 Q9Y2H9.1 Q504T8.1 Q8N183.1 P03107.1 P26539.1 P36745.1 P50799.1Q81023.1 Q8TCT9.1 Q9H2D1.1 O60830.1 O94826.1 Q8IWA4.1 P28482.1 Q16584.1O43318.1 O43683.1 Q9Y3D0.1 P08571.1 E7EWX8.1 Q99549.1 Q04360.1 Q96T58.1Q8WX17.1 Q9H8L6.1 P11229.1 P20309.1 Q5VZF2.1 O00499.1 P01106.1 P02687.1P25188.1 P25274.1 P81558.1 F7A0B0.1 P02686.1 P02689.1 P25189.1 P60201.1P60202.1 P20916.1 Q13875.1 E9PG44.1 Q16653.1 Q5SUK5.1 P24158.1 P41218.1Q969H8.1 Q8WXC6.1 P05164.1 Q9NPC7.1 Q9H1R3.1 P35749.1 P35579.1 Q09013.1O95248.1 O14745.1 O84639.1 P15586.1 P54450.1 Q8IXJ6.1 O95167.1 O95298.1P19404.1 O75251.1 Q6N069.1 Q73WP1.1 Q86VF7.1 Q9BT67.1 O75113.1 Q15843.1Q13564.1 Q8IXH7.1 P58400.1 P58401.1 Q09666.1 P12036.1 P07196.1 P07197.1Q8NEJ9.1 Q13491.1 P59665.1 P08246.1 Q9Y6K9.1 Q9NV10.1 P43490.1 Q14112.1Q5JPE7.1 P69849.1 O95897.1 Q13253.1 P05114.1 P05204.1 P80272.1 Q15233.1P29597.1 P23497.1 P08651.1 Q14938.1 Q16236.1 P19838.1 Q6P4R8.1 O75694.1P52948.1 P11654.1 Q8TEM1.1 Q9QY81.1 B4DW92.1 Q9Y6Q9.1 Q9H1E3.1 P67809.1Q9H8H0.1 P78316.1 O00567.1 Q9Y2X3.1 Q9NR30.1 P19338.1 O75607.1 Q8NFH5.1P03466.1 P0C025.1 Q99733.1 Q12830.1 Q96RS6.1 Q9H209.1 A6NMS3.1 P23515.1Q9HD40.1 295413917.1 295413964.1 295441897.1 Q9PWU2.1 P0C675.1 P11926.1P54368.1 P10451.1 A2T3P5.1 A2T3T2.1 Q8TAD7.1 Q9BXB4.1 Q9UBL9.1 P03262.1Q96ST3.1 P50897.1 Q8IXS6.1 Q6ZV29.1 Q6ZW49.1 Q9UBV8.1 Q15154.1 O60664.1Q01453.1 O60437.1 P32119.1 O43808.1 Q13794.1 Q9H2J4.1 Q8IZ21.1 Q92903.1O95674.1 Q9UKL6.1 P04180.1 P30086.1 O00329.1 P42356.1 O14986.1 P57054.1O95394.1 E4NG02.1 P00558.1 P18669.1 P15259.1 Q96FE7.1 Q9Y263.1 Q13393.1P26276.1 Q2FZ93.1 B2RID6.1 Q9Y617.1 P05155.1 P00747.1 O25249.1 P13796.1P07359.1 P16234.1 Q96CS7.1 Q9H7P9.1 Q15149.1 O43660.1 Q8IUK5.1 Q6UX71.1P09874.1 Q460N5.1 Q9UKK3.1 Q15365.1 Q15366.1 Q9BY77.1 A6Q6E9.1 B2RGP7.1295413956.1 I6XH73.1 Q96FM1.1 O43525.1 P19156.1 P18434.1 P0CG38.1Q16633.1 O84616.1 O75915.1 O84647.1 P68950.1 P02545.1 Q6P2Q9.1 O43143.1Q9HCS7.1 Q961Z0.1 P9WQ27.1 O84288.1 Q92841.1 Q15751.1 Q7Z333.1 O84419.1O84818.1 B2RJ72.1 Q8N0Y7.1 O60312.1 Q9UHA3.1 P89479.1 Q9H3G5.1 Q02809.1P07737.1 Q8WUM4.1 Q53EL6.1 P49683.1 P12004.1 Q9UQ80.1 Q7Z6L0.1 Q07954.1P13674.1 C9JIZ6.1 Q9H7Z7.1 P40306.1 P49720.1 P28074.1 O60678.1 O14744.1P03189.1 P78543.1 O75629.1 O84583.1 O60888.1 P30101.1 Q14554.1 Q96JJ7.1P03129.1 Q9H8V3.1 Q96PZ2.1 Q8WU58.1 Q96IP4.1 Q92636.1 Q96JP0.1 Q4ZG55.1Q9ULI3.1 Q96ST2.1 Q7Z3U7.1 P33215.1 Q8NHV4.1 Q9UFN0.1 O60502.1 Q6UWS5.1Q86U86.1 P23297.1 P60903.1 P06702.1 P04271.1 Q9UPN6.1 Q6P126.1 Q6ZMD2.1Q9BVV6.1 P14079.1 Q8WUY1.1 P50616.1 O15027.1 Q15436.1 Q15437.1 D4ACF2.1Q9QJ57.1 Q9QJ42.1 Q70J99.1 Q9GZT5.1 B1AQ67.1 Q9UM07.1 P21980.1 Q92954.1Q96JQ0.1 Q9JZQ0.1 A6NMY6.1 Q6FDV9.1 Q5VTE0.1 548558395.1 Q2VIR3.1Q58FF8.1 Q9HCE1.1 P13985.1 A2RGE9.1 Q8IXJ9.1 Q6P2P2.1 D3HT40.1 P42588.156160925.1 Q53H96.1 P08559.1 H0YD97.1 O00330.1 P14618.1 Q9BXR0.1Q9H974.1 Q9H2M9.1 P35241.1 Q14699.1 P0DJD1.1 Q9BYM8.1 A6NK89.1 P61106.1B2RHG7.1 P04626.1 Q13546.1 Q92932.1 Q16849.1 P78509.1 P03209.1 P35249.1P15927.1 P27694.1 O75678.1 Q14257.1 Q9NQC3.1 Q9BZR6.1 P10276.1 P10826.1P49788.1 Q8TC12.1 P10745.1 P02753.1 P52566.1 Q7Z616.1 Q9BRR9.1 Q15052.1Q81Y67.1 P11908.1 Q15418.1 Q9UK32.1 O43159.1 Q9ULK6.1 Q7L0R7.1 Q9C0B0.1Q9H0A0.1 O00472.1 P18333.1 Q6PD62.1 Q9NTZ6.1 Q5T481.1 Q96EV2.1 Q9BQ04.1P35637.1 Q9UKM9.1 P22087.1 Q9Y230.1 P31153.1 Q9NSC2.1 O94885.1 Q93084.1P08168.1 P10523.1 Q9BQB4.1 O14828.1 Q13018.1 Q9UHJ6.1 Q9H4L4.1 Q9GZR1.1Q15019.1 Q14141.1 O15270.1 Q92743.1 O43464.1 P49842.1 Q9BZL6.1 O15075.1Q96GX5.1 Q8TD19.1 Q13153.1 F5GWT4.1 P63151.1 A6PVN5.1 Q06190.1 P53041.1Q8N8A2.1 Q13315.1 P49591.1 Q86SQ7.1 P02787.1 P36952.1 Q14140.1 B7WNR0.1P02768.1 Q9BYB0.1 Q5T123.1 Q9BZZ2.1 P67812.1 Q9BY50.1 P61009.1 P37108.1P42224.1 Q92783.1 Q96FS4.1 Q9UIB8.1 O75094.1 Q55732.1 O00193.1 Q7Z3B0.1P62304.1 P62306.1 P62308.1 P62314.1 P62316.1 P62318.1 P63162.1 P14678.1P53814.1 Q13573.1 Q63008.1 P05023.1 Q96K37.1 Q9NQZ2.1 Q96L92.1 Q14515.1Q13813.1 Q01082.1 P63208.1 P21453.1 P23246.1 M5JGM9.1 Q9NY15.1 Q7KZF4.1Q9NQZ5.1 P16949.1 P05093.1 P08686.1 P36956.1 Q12772.1 Q7Z7C7.1 Q96BY9.1P38646.1 P08254.1 Q14683.1 O95347.1 Q8IY18.1 P07566.1 P51649.1 P14410.1O00391.1 O75897.1 Q8NDZ2.1 P00441.1 O14512.1 Q8IWZ8.1 Q6UWL2.1 Q8TAQ2.1O15056.1 P60880.1 Q9UQF0.1 O15400.1 Q9UNK0.1 B4DHN5.1 O00560.1 Q16635.1Q9Y490.1 Q8N9U0.1 O95271.1 D3YTG3.1 Q7Z7G0.1 Q9ULW0.1 P13686.1 Q86VP1.1Q96F92.1 Q4KMP7.1 Q9UL17.1 P01730.1 Q99832.1 F5H7V9.1 P24821.1 Q9UKZ4.1Q5VYS8.1 Q92563.1 Q8N6V9.1 Q9Y6M0.1 P04958.1 P05452.1 Q8NBS9.1 Q86V81.1Q86YJ6.1 Q5VV42.1 P40225.1 P07996.1 P35442.1 P04818.1 P63313.1 P62328.1P01266.1 H7C1F5.1 P07202.1 P16473.1 P21463.1 Q07157.1 Q9NR96.1 J3KNT7.1Q9Y2L5.1 P03206.1 P37837.1 P20062.1 P51532.1 Q14241.1 Q7KZ85.1 P05412.1A0AVK6.1 Q14469.1 P31629.1 P17275.1 Q8NHW3.1 Q9ULX9.1 P35716.1 Q06945.1P57073.1 Q02447.1 Q02446.1 O15164.1 Q9BWW7.1 Q04726.1 Q04727.1 P02786.1Q9Y4A5.1 P01137.1 Q15582.1 P61586.1 P37802.1 P29401.1 P69222.1 Q92616.1P51571.1 Q14956.1 Q96GE9.1 P57088.1 Q9BXS4.1 Q9C0B7.1 Q9Y5L0.1 P02766.1Q13428.1 Q5T2D2.1 Q07283.1 P22102.1 A2RCL1.1 Q8NDV7.1 Q6P9F5.1 Q6ZTA4.1P04295.1 O14773.1 Q97HE9.1 Q9Y3I0.1 P17752.1 Q8IWU9.1 Q0VAP8.1 P68363.1Q9BQE3.1 P07437.1 Q9H4B7.1 Q13885.1 Q13509.1 P04350.1 P68371.1 Q9BUF5.1Q14679.1 O75347.1 O14788.1 P48023.1 P43489.1 P25445.1 Q8N726.1 Q99816.1Q15672.1 P14679.1 P07101.1 P23458.1 Q9Y2R2.1 P29350.1 P78324.1 P08621.1P17133.1 Q62376.1 P09012.1 P09234.1 O75643.1 Q9UMX0.1 Q9UHD9.1 Q9Y4E8.1Q9UPT9.1 Q8NFA0.1 Q86T82.1 Q86UV5.1 O15205.1 P62979.1 H0Y5H6.1 Q14157.1O00762.1 Q96LR5.1 P62253.1 P22314.1 A0AVT1.1 Q15386.1 Q92575.1 I6ZLG2.1O15294.1 Q9DUC0.1 Q6ZRI6.1 Q9NSG2.1 Q9BWL3.1 Q9NZ63.1 P0C727.1 Q9ZDE9.1Q89882.1 P39999.1 Q12965.1 A2A306.1 A2RGM0.1 A6NG79.1 B8ZS71.1 B8ZUA4.1E7EPZ9.1 F8W7G7.1 H0Y335.1 J3KP29.1 M7PC26.1 M7PDR8.1 M7Q4Y3.1 Q5T8M8.1Q7TWS5.1 S5U6K1.1 S5UMF6.1 S5USV8.1 W5Z3U0.1 Q9BSU1.1 Q49AR2.1 P69996.1P06132.1 Q709C8.1 O75436.1 Q9UBQ0.1 Q96AX1.1 P32241.1 Q3ASL6.1 Q00341.1P08670.1 P03180.1 P02774.1 P04004.1 Q01668.1 O00555.1 P27884.1 O43497.1P04275.1 Q9Y279.1 Q16864.1 O75348.1 Q2M389.1 O75083.1 Q9UNX4.1 C9J016.1Q8IWA0.1 Q6UXN9.1 Q2TAY7.1 P13010.1 P12956.1 Q9Y2T7.1 A1JUA3.1 O95625.1Q8NAP3.1 Q96K80.1 Q9Y6R6.1 Q01954.1 Q9P243.1 Q96KR1.1 Q8IWU4.1 P25311.1

Predicting the Immunological Response of an Individual to a PolypeptideAntigen

Specific polypeptide antigens induce immune responses in only a fractionof human subjects. Currently, there is no diagnostic test that canpredict whether a polypeptide antigen would likely induce an immuneresponse in an individual. In particular, there is a need for a testthat can predict whether a person is an immune responder to a vaccine orimmunotherapy composition.

According to the present disclosure, the polypeptide antigen-specific Tcell response of an individual is defined by the presence within thepolypeptide of one or more fragments that may be presented by multipleHLA class I or multiple HLA class II molecules of the individual.

In some cases the disclosure involves a method of predicting whether asubject will have an immune response to administration of a polypeptide,wherein an immune response is predicted if the polypeptide isimmunogenic according to any method described herein. A cytotoxic T cellresponse is predicted if the polypeptide comprises at least one aminoacid sequence that is a T cell epitope capable of binding to at leasttwo HLA class I molecules of the subject. A helper T cell response ispredicted if the polypeptide comprises at least one amino acid sequencethat is a T cell epitope capable of binding to at least two HLA class IImolecules of the subject. No cytotoxic T cell response is predicted ifthe polypeptide does not comprise any amino acid sequence that is a Tcell epitope capable of binding to at least two HLA class I molecules ofthe subject. No helper T cell response is predicted if the polypeptidedoes not comprise any amino acid sequence that is a T cell epitopecapable of binding to at least two HLA class II molecules of thesubject.

In some cases the polypeptide is an active component of a pharmaceuticalcomposition, and the method comprises predicting the development orproduction of anti-drug antibodies (ADA) to the polypeptide. Thepharmaceutical composition may be a drug selected from those listed inTable 8. According to the present disclosure, ADA development will occurif, or to the extent that, an active component polypeptide is recognisedby multiple HLA class II molecules of the subject, resulting in a helperT cell response to support an antibody response to the active component.The presence of such epitopes (PEPIs) may predict the development of ADAin the subject. The method may further comprise selecting orrecommending for treatment of the human subject administration to thesubject of a pharmaceutical composition that is predicted to induce lowor no ADA, and optionally further administering the composition to thesubject. In other cases the method predicts that the pharmaceuticalcomposition will induce unacceptable ADA and the method furthercomprises selecting or recommending or treating the subject with adifferent treatment or therapy. The polypeptide may be a checkpointinhibitor. The method may comprise predicting whether the subject willrespond to treatment with the checkpoint inhibitor.

TABLE 8 Example drugs associated with ADA-related adverse events DrugADA-related adverse event Abciximab anaphylaxis Adalimumab anti-drugantibodies and treatment failure Basiliximab anaphylaxis Cetuximab IgE,anaphlyaxis Epoetin Antibody-mediated pure red cell aplasiaErythropoietin pure red cell aplasia Etanercept no apparent effect onsafety Factor-IX anaphylaxis Infliximab anaphylaxis OKT3 anaphylaxisPegloticase anti-dug antibody, treatment failure rIFN-beta anaphylaxisrecombinant factor VIII anaphylaxis Thrombopoietin thrombocitopeniaUstekinumab anti-ustekinumab antibodies, affected treatment efficacy

There is also currently no test that can predict the likelihood that aperson will have a clinical response to, or derive clinical benefitfrom, a vaccine or immunotherapy composition. This is important becausecurrently T cell responses measured in a cohort of individualsparticipating in vaccine or immunotherapy clinical trials poorlycorrelate with clinical responses. That is, the clinical respondersubpopulation is substantially smaller than the immune respondersubpopulation. Therefore, to enable the personalization of vaccines andimmunotherapies it is important to predict not only the likelihood of animmune response in a specific subject, but also whether the immuneresponse induced by the drug will be clinically effective (e.g. can killcancer cells or pathogen infected cells or pathogens).

The presence in a vaccine or immunotherapy composition of at least twopolypeptide fragments (epitopes) that can bind to at least three HLAclass I of an individual (≥2 PEPI3+) is predictive for a clinicalresponse. In other words, if ≥2 PEPI3+ can be identified within theactive ingredient polypeptide(s) of a vaccine or immunotherapycomposition, then an individual is a likely clinical responder. A“clinical response” or “clinical benefit” as used herein may be theprevention of or a delay in the onset of a disease or condition, theamelioration of one or more symptoms, the induction or prolonging ofremission, or the delay of a relapse or recurrence or deterioration, orany other improvement or stabilisation in the disease status of asubject. Where appropriate, a “clinical response” may correlate to“disease control” or an “objective response” as defined by the ResponseEvaluation Criteria In Solid Tumors (RECIST) guidelines.

In some cases the disclosure involves a method of predicting whether thesubject will have a clinical response to administration of apharmaceutical composition such as a vaccine or immunotherapycomposition comprising one or more polypeptides as active ingredients.The method may comprise determining whether the one or more polypeptidestogether comprise at least two different sequences each of which is a Tcell epitope capable of binding to at least two, or in some cases atleast three HLA class I molecules of the subject; and predicting thatthe subject will have a clinical response to administration of thepharmaceutical composition if the one or more polypeptides togethercomprise at least two different sequences each of which is a T cellepitope capable of binding to at least two, or in some cases at leastthree HLA class I molecules of the subject; or that the subject will nothave a clinical response to administration of the pharmaceuticalcomposition if the one or more polypeptides together comprise no morethat one sequence that is a T cell epitope capable of binding to atleast two, or in some cases at least three HLA class I molecules of thesubject.

For the purposes of this method two T cell epitopes are “different” fromeach other if they have different sequences, and in some cases also ifthey have the same sequence that is repeated in a target polypeptideantigen. In some cases the different T cell epitopes in a targetpolypeptide antigen do not overlap with one another.

In some cases all of the fragments of one or more polypeptides or activeingredient polypeptides that are immunogenic for a human subject areidentified using the methods described herein. The identification of atleast one fragment of the polypeptide(s) that is a T cell epitopecapable of binding to at least two, or at least three HLA class Imolecules of the subject predicts that the polypeptide(s) will elicit oris likely to elicit a cytotoxic T cell response in the subject. Theidentification of at least one fragment of the polypeptide(s) that is aT cell epitope capable of binding to at least two, or at least three, orat least four HLA class II molecules of the subject predicts that thepolypeptide(s) will elicit or is likely to elicit a helper T cellresponse in the subject. The identification of no fragments of thepolypeptide(s) that are T cell epitopes capable of binding to at leasttwo, or at least three HLA class I molecules of the subject predictsthat the polypeptide(s) will not elicit or is not likely to elicit acytotoxic T cell response in the subject. The identification of nofragments of the polypeptide(s) that are T cell epitopes capable ofbinding to at least two, or at least three, or at least four HLA classII molecules of the subject predicts that the polypeptide(s) will notelicit or is not likely to elicit a helper T cell response in thesubject. The identification of at least two fragments of one or moreactive ingredient polypeptides of a vaccine or immunotherapycomposition, wherein each fragment is a T cell epitope capable ofbinding to at least two, or at least three HLA class I molecules of thesubject predicts that the subject is more likely to have, or will have aclinical response to the composition. The identification of less thantwo fragments of the one or more polypeptides that are T cell epitopescapable of binding to at least two, or at least three HLA class Imolecules of the subject predicts that the subject is less likely tohave, or will not have, a clinical response to the composition.

Without wishing to be bound by theory, one reason for the increasedlikelihood of deriving clinical benefit from a vaccine/immunotherapycomprising at least two multiple-HLA binding PEPIs, is that diseasedcell populations, such as cancer or tumor cells or cells infected byviruses or pathogens such as HIV, are often heterogenous both within andbetween affected subjects. A specific cancer patient, for example, mayor may not express or overexpress a particular cancer associated targetpolypeptide antigen of a vaccine, or their cancer may compriseheterogeneous cell populations, some of which (over-)express the antigenand some of which do not. In addition, the likelihood of developingresistance is decreased when more multiple HLA-binding PEPIs areincluded or targeted by a vaccine/immunotherapy because a patient isless likely to develop resistance to the composition through mutation ofthe target PEPI(s).

The likelihood that a subject will respond to treatment is thereforeincreased by (i) the presence of more multiple HLA-binding PEPIs in theactive ingredient polypeptides; (ii) the presence of PEPIs in moretarget polypeptide antigens; and (iii) (over-)expression of the targetpolypeptide antigens in the subject or in diseased cells of the subject.In some cases expression of the target polypeptide antigens in thesubject may be known, for example if target polypeptide antigens are ina sample obtained from the subject. In other cases, the probability thata specific subject, or diseased cells of a specific subject,(over-)express a specific or any combination of target polypeptideantigens may be determined using population expression frequency data.The population expression frequency data may relate to a subject- and/ordisease-matched population or the intent-to-treat population. Forexample, the frequency or probability of expression of a particularcancer-associated antigen in a particular cancer or subject having aparticular cancer, for example breast cancer, can be determined bydetecting the antigen in tumor, e.g. breast cancer tumor samples. Insome cases such expression frequencies may be determined from publishedfigures and scientific publications. In some cases a method of theinvention comprises a step of determining the expression frequency of arelevant target polypeptide antigen in a relevant population.

Disclosed is a range of pharmacodynamic biomarkers to predict theactivity/effect of vaccines in individual human subjects as well as inpopulations of human subjects. The biomarkers have been developedspecifically for cancer vaccines, but similar biomarkers could be usedfor other vaccines or immunotherapy compositions. These biomarkersexpedite more effective vaccine development and also decrease thedevelopment cost and may be used to assess and compare differentcompositions. Exemplary biomarkers are as follows.

-   -   AG95—potency of a vaccine: The number of antigens in a cancer        vaccine that a specific tumor type expresses with 95%        probability. AG95 is an indicator of the vaccine's potency, and        is independent of the immunogenicity of the vaccine antigens.        AG95 is calculated from the tumor antigen expression rate data.        Such data may be obtained from experiments published in peer        reviewed scientific journals. Technically, AG95 is determined        from the binomial distribution of antigens in the vaccine, and        takes into account all possible variations and expression rates.    -   PEPI3+ count—immunogenicity of a vaccine in a subject:        Vaccine-derived PEPI3+ are personal epitopes that bind to et        least 3 HLAs of a subject and induce T cell responses. PEPI3+        can be determined using the PEPI3+ Test in subjects who's        complete 4-digit HLA genotype is known.    -   AP count—antigenicity of a vaccine in a subject: Number of        vaccine antigens with PEPI3+. Vaccines contain sequences from        target polypeptide antigens expressed by diseased cells. AP        count is the number of antigens in the vaccine that contain        PEPI3+, and the AP count represents the number of antigens in        the vaccine that can induce T cell responses in a subject. AP        count characterizes the vaccine-antigen specific T cell        responses of the subject since it depends only on the HLA        genotype of the subject and is independent of the subject's        disease, age, and medication. The correct value is between 0 (no        PEPI presented by the antigen) and maximum number of antigens        (all antigens present PEPIs).    -   AP50—antigenicity of a vaccine in a population: The mean number        of vaccine antigens with a PEPI in a population. The AP50 is        suitable for the characterization of vaccine-antigen specific T        cell responses in a given population since it depends on the HLA        genotype of subjects in a population.    -   AGP count—effectiveness of a vaccine in a subject: Number of        vaccine antigens expressed in the tumor with PEPI. The AGP count        indicates the number of tumor antigens that vaccine recognizes        and induces a T cell response against (hit the target). The AGP        count depends on the vaccine-antigen expression rate in the        subject's tumor and the HLA genotype of the subject. The correct        value is between 0 (no PEPI presented by expressed antigen) and        maximum number of antigens (all antigens are expressed and        present a PEPI).    -   AGP50—effectiveness of a cancer vaccine in a population: The        mean number of vaccine antigens expressed in the indicated tumor        with PEPI (i.e., AGP) in a population. The AGP50 indicates the        mean number of tumor antigens that the T cell responses induced        by the vaccine can recognize. AGP50 is dependent on the        expression rate of the antigens in the indicated tumor type and        the immunogenicity of the antigens in the target population.        AGP50 can estimate a vaccine's effectiveness in different        populations and can be used to compare different vaccines in the        same population. The computation of AGP50 is similar to that        used for AG50, except the expression is weighted by the        occurrence of the PEPI3+ in the subject on the expressed vaccine        antigens. In a theoretical population, where each subject has a        PEPI from each vaccine antigen, the AGP50 will be equal to AG50.        In another theoretical population, where no subject has a PEPI        from any vaccine antigen, the AGP50 will be 0. In general, the        following statement is valid: 0≤AGP50≤AG50.    -   mAGP—a candidate biomarker for the selection of likely        responders: Likelihood that a cancer vaccine induces T cell        responses against multiple antigens expressed in the indicated        tumor. mAGP is calculated from the expression rates of        vaccine-antigens in e.g. the tumor and the presence of vaccine        derived PEPIs in the subject. Technically, based on the AGP        distribution, the mAGP is the sum of probabilities of the        multiple AGP (≥2 AGPs).

The results of a prediction as set out above may be used to inform aphysician's decisions concerning treatment of the subject. Accordingly,in some cases the polypeptide is an active ingredient, for example of avaccine or immunotherapy composition, the method of the disclosurepredicts that the subject will have, is likely to have, or has above athreshold minimum likelihood of having an immune response and/or aclinical response to a treatment comprising administering the activeingredient polypeptide to the subject, and the method further comprisesselecting the treatment for or selecting the vaccine or immunotherapycomposition for treatment of the specific human subject. Also providedis a method of treatment with a subject-specific pharmaceuticalcomposition, kit or panel of polypeptides comprising one or morepolypeptides as active ingredients, wherein the pharmaceuticalcomposition, kit or panel of polypeptides has been determined to have athreshold minimum likelihood of inducing a clinical response in thesubject, wherein the likelihood of response has been determined using amethod described herein. In some cases the minimum threshold is definedby one or more of the pharmacodynamic biomarkers described herein, forexample a minimum PEPI3+ count (for example 2, 3, 4, 5, 6, 7, 8, 9, 10,11, or 12 or more PEPI3+), a minimum AGP count (for example AGP=at least2 or at least 3, 4, 5, 6, 7, 8, 9, 10, 11, or 12 or more) and/or aminimum mAGP (for example AGP=at least 2 or at least 3, 4, 5, 6, 7, 8,9, 10, 11, or 12 or more). For example, in some cases a subject isselected for treatment if their likelihood of a response targeted at apredefined number of target polypeptide antigens, optionally wherein thetarget polypeptide antigens are (predicted to be) expressed, is above apredetermined threshold (e.g. 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, or 12 ormore). Alternatively, the method may predict that the one or morepolypeptide(s) of the composition will not elicit a T cell responseand/or a clinical response in the subject and further comprise selectinga different treatment for the subject.

Predicting an Autoimmune or Toxic Immune Response to a PolypeptideAntigen

The differences among HLAs may influence the probability that a subjectwill experience immune-toxicity from a drug or polypeptide administeredto the subject. There may be a toxic immune response if a polypeptideadministered to the subject comprises a fragment that corresponds to afragment of an antigen expressed in normal healthy cells of the subjectand that comprises an amino acid that is a T cell epitope capable ofbinding to multiple HLA class I molecules of the subject. Therefore,some cases in accordance with the disclosure, involve identifying atoxic immunogenic region or fragment of a polypeptide or identifyingsubjects who are likely to experience immune-toxicity in response toadministration of one or more polypeptides or a fragments thereof. Thepolypeptide may be an active ingredient of a vaccine or immunotherapycomposition as described herein.

The method may comprise determining whether the polypeptide(s) comprisesa sequence that is a T cell epitope capable of binding to at least two,or in other cases to at least three HLA class I molecules of thesubject. In some cases the method comprises determining that thepolypeptide comprises a sequence that is a T cell epitope capable ofbinding to at least four, or at least five HLA class I molecules of thesubject; or an amino acid sequence that is a T cell epitope capable ofbinding to at least four, or at least five, or at least six or at leastseven HLA class II of the subject. The method may further compriseidentifying said sequence as toxic immunogenic for the subject orpredicting a toxic immune response in the subject. In other cases nosuch amino acid sequence is identified and the method further comprisespredicting no toxic immune response in the subject. The method mayfurther comprise selecting or recommending for treatment of the subjectadministration of one or more polypeptides or a pharmaceuticalcomposition that is predicted to induce no or low immune-toxicity, andoptionally further treating the subject by administering thepolypeptide. The disclosure also provides a method of treating a subjectin need thereof by administrating to the subject such a polypeptide orcomposition.

In some cases a method described herein further comprises mutating apolypeptide that is predicted to be immunogenic for a subject, or thatis predicted to be immunogenic in a proportion of subjects in a humanpopulation. Also provided is a method of reducing the immunogenicity ofa polypeptide that has been identified as immunogenic in a subject or ina proportion of a human population as described herein. The polypeptidemay be mutated to reduce the number of PEPIs in the polypeptide or toreduce the number of HLA class I or class II molecules of the subject orof said population that bind to the fragment of the polypeptide that isidentified as immunogenic in the subject or in a proportion of saidpopulation. In some cases the mutation may reduce or prevent a toxicimmune response or may increase the efficacy by preventing the ADAdevelopment in the subject or in a proportion of said population. Themutated polypeptide may be further selected or recommended for treatmentof the subject or of a subject of said population. The subject mayfurther be treated by administration of the mutated polypeptide. Thedisclosure also provides a method of treating a subject in need thereofby administrating to the subject such a mutated polypeptide.

Predicting the Immunological Response of a Human Population to aPolypeptide Antigen

The methods described herein may be used to predict the response orresponse rate of a wider human population to administration of one ormore polypeptides or compositions comprising one or more polypeptides.In some cases a method of the disclosure may be repeated for a pluralityof human subjects to predict the response or response rate in thosesubjects. In other cases the method of the disclosure may be repeatedfor each subject in a relevant sample or model population of subjectsand the results used to predict or define the response or response ratein a broader human population represented by the sample or modelpopulation. The sample/model population may be relevant to theintent-to-treat population for a pharmaceutical composition. A relevantpopulation is one that is representative or similar to the populationfor whom or amongst whom treatment with the pharmaceutical compositionis intended. In some cases the sample/model population is representativefor the whole human race. In other cases the sample/model population maybe disease- or subject-matched to the broader population(subpopulation), for example by ethnicity, geographical location,gender, age, disease or cancer, disease or cancer type or stage,genotype, expression of one or more biomarkers, partially by HLAgenotype (for example subjects have one or more particular HLA alleles).For example, the sample/model population may have HLA class I and/orclass II genomes that are representative of those found in the worldpopulation, or in subjects having a particular disease or condition, orethnic background, from a particular geographical location, or having aparticular disease-associated biomarker (for example, women having theBRCA mutation for a breast cancer vaccine). In some cases thesample/model population is representative for at least 70%, or 75% or80% or 84% or 85% or 86% or 90% or 95% of the broader population by HLAdiversity and/or HLA frequency.

The method may comprise the step of selecting or defining a relevantsample or model population. Each subject in the sample/model populationis minimally defined by their HLA class I or class II genotype, e.g.complete 4-digit HLA class I genotype. Data concerning the HLA genotypeof the sample/model population may be stored or recorded in or retrievedfrom a database or be an in silico model human population.

In some cases the methods described herein may be used to conduct an insilico clinical trial that predicts the proportion of immune-respondersor the proportion of clinical responders in a population for a givendrug, such as a vaccine or immunotherapy composition. This is useful forpre-selecting drugs that are likely to have high rates of efficacy toundergo clinical testing.

A population of individuals or a subpopulation of individuals cancomprise the study cohort of an in silico clinical trial conducted witha drug. Each individual in the study cohort is characterized by its HLAgenotype. The proportion of individuals in the study cohort having ≥1PEPI2+, or ≥1 PEPI3+, or ≥1 PEPI4+, or ≥1 PEPI5+, derived from thepolypeptides of the drug may be calculated. For the purposes of thisdisclosure we have termed this the “PEPI Score”. Unless otherwiseindicted, the “PEPI Score” refers specifically to the ≥1 PEPI3+ Score.This PEPI Score predicts the proportion of subjects with T cellresponses in a clinical trial conducted with the same drug in a relevantcohort of subjects.

The disclosure provides a method of conducting an in silico trial for avaccine or immunotherapy composition having one or more polypeptideactive ingredients. The in silico trial may predict the cytotoxic T cellresponse rate of a human population. The method may comprise: (i)selecting or defining an in silico model human population comprising aplurality of subjects each defined by HLA class I genotype, wherein thein silico model human population may correspond to or be representativeof, or relevant to the intend-to-treat, said human population in whichthe cytotoxic T cell response rate is to be predicted; (ii) determiningfor each subject in the in silico model human population whether the oneor more active ingredient polypeptides comprise at least one sequencethat is PEPI2+, PEPI3+, PEPI4+ or PEPI5+(depending the size,administration route and adjuvants of the polypeptide composition); and(iii) predicting the cytotoxic T cell response rate (of said humanpopulation), wherein a higher proportion of the in silico model humanpopulation that meet the requirements of step (ii) predicts a highercytotoxic T cell response rate. The proportion of the in silico modelhuman population that meet the requirements of step (ii) may correlatewith or correspond to the predicted response rate in the intend-to-treatpopulation.

Correlation between the presence of HLA-restricted epitopes and immuneresponse rates and/or clinical response rates has not been demonstratedby clinical trials of the prior art. This raises the question about themechanism of action of immunotherapies. The Examples provided hereinshow that activation of cytotoxic T lymphocytes (CTLs) against multipletargets may be required for a clinically meaningful response, forexample against heterogeneous tumors. So far, CTL responses reported inclinical trials neither account for multiple targets nor for multipleHLAs. For example, a melanoma peptide vaccine targeting two antigens(Tyrosinase and gp100) elicited CTL responses in 52% of patients, butonly 12% had clinical benefit. Using an in silico Model Population of433 subjects we determined a ≥1 PEPI3+ Score of 42% (in 42% at least onevaccine-derived epitope could be identified that could be presented byat least three HLA class I of the subject) and a ≥2 PEPI3+ Score of 6%(in 6% at least two vaccine-derived epitopes could be identified thatcould be presented by at least three HLA class II of the subject). Thisexplains why the clinical investigators did not find correlation betweenCTL response rate and clinical response rate in their trial: thepeptides in the vaccine performed poorly in the trial because there wereonly a few patients in which two different vaccine peptides could bothactivate CTL responses. The discrepancy between the results of theclinical trial and our in silico trial is based on the differentpopulations, since the populations of each had subjects with differentHLA genotypes. However, the response rate results provided by the insilico trial on the Model Population are a good prediction for theresponse rate outcome in the clinical trial population.

Therefore disclosed herein is a method of conducting an in silico trialfor a vaccine or immunotherapy composition having one or more activeingredient polypeptides. The in silico trial may predict the clinicalresponse rate of a human population. The method may comprise (i)selecting or defining an in silco model human population comprising aplurality of subjects defined by HLA class I genotype, wherein the insilico model human population may correspond to or be representative ofsaid human population (relevant to the intend-to-treat population) inwhich the clinical response rate is to be predicted; (ii) determiningfor each subject in the in silico model human population whether the oneor more active ingredient polypeptides comprise at least two differentsequences each of which is a T cell epitope capable of binding to atleast three, or at least four, or at least five HLA class I of thesubject; and (iii) predicting the clinical response rate (of said humanpopulation), wherein a higher proportion of the in silico model humanpopulation that meet the requirements of step (ii) predicts a higherclinical response rate. The proportion of the in silico model humanpopulation that meet the requirements of step (ii) may correlate with orcorrespond to the predicted response rate in the intend-to-treatpopulation.

An equivalent method may be used to predict, for example, the immunetoxicity rate, checkpoint inhibitor response rate, ADA development rate,or helper T cell response rate of a human population (or subpopulation)to administration of a polypeptide or pharmaceutical compositioncomprising one or more polypeptides as active ingredients.

In some cases the method may be repeated for one or more furtherpolypeptides or fragments thereof or vaccine or pharmaceutical orimmunotherapy compositions. The polypeptides, fragments or compositionsmay be ranked according to their predicted response rates in said humanpopulation. This method is useful for selecting the most effective ormost safe polypeptide drugs for the intent-to-treat population.

Design and Preparation of Pharmaceutical Compositions

In some aspects the disclosure provides a method of designing orpreparing a polypeptide, or a polynucleic acid that encodes apolypeptide, for inducing an immune response, a cytotoxic T cellresponse or a helper T cell response in a human subject (e.g. in atarget or intent-to-treat population). The disclosure also provides animmunogenic composition, or pharmaceutical composition, kit or panel ofpeptides, methods of designing or preparing the same, compositions thatmay be obtained by those methods, and their use in a method of inducingan immune response, a cytotoxic T cell response, or a helper T cellresponse in the subject, or a method of treating, vaccinating orproviding immunotherapy to a subject.

The methods involve identifying and/or selecting a T cell epitope thatbinds to multiple, e.g. at least three HLA class I molecules ofindividual subjects across the target population with a high frequency,and designing or/or preparing a polypeptide that comprises one or moresuch epitopes (PEPI3+s). Such high frequency population PEPI3+s may bereferred to herein as “bestEPIs”. According to the present disclosurebestEPIs induce immune responses in a high proportion of human subjectsin the specific or target human population. The polypeptide may be anactive ingredient in a pharmaceutical composition or kit or panel ofpolypeptides for use in a method of treatment of a subject of thespecific or target human population.

The composition/kit may optionally further comprise at least onepharmaceutically acceptable diluent, carrier, or preservative and/oradditional polypeptides that do not comprise any bestEPIs. Thepolypeptides may be engineered or non-naturally occurring. The kit maycomprise one or more separate containers each containing one or more ofthe active ingredient peptides. The composition/kit may be apersonalised medicine to prevent, diagnose, alleviate, treat, or cure adisease of an individual, such as a cancer.

In some cases the bestEPI is capable of binding to multiple, for exampleto at least three HLA class I and/or to at least three HLA class IImolecules of a high percentage of the subjects in a sample or modelpopulation, such as described herein. In some cases a “high” percentagemay be at least or more than 1%, 2%, 5%, 10%, 12%, 15%, 16%, 17%, 18%,19%, 20%, 21%, 22%, 23%, 24%, 25%, 26%, 27%, 28%, 29%, 30%, 31%, 32%,33%, 34%, 35%, 36%, 37%, 38%, 39%, 40%, 41%, 42%, 43%, 44%, 45%, 46%,47%, 48%, 49% or 50% of the relevant population or subpopulation ofhuman subjects. In some cases a “high” percentage is relative to thepercentage of subjects in the population having other PEPI3+s. Forexample, the PEPI3+ may be the most frequent in the population, or morefrequent than 50%, or 55% or 60% or 65% or 70% or 75% or 80% or 85% or90% or 95% or 97% or 99% of all PEPI3+ and/or PEPI4+ and/or PEPI4+ inone or more reference target polypeptide antigens.

In some cases the probability that the target polypeptide antigen isexpressed in a subject of the specific or target population is takeninto account to determine the overall likelihood that the bestEPI willinduce an immune response that targets a polypeptide antigen that isexpressed by a subject of the specific or target human population. Insome cases the bestEPI is predicted to express both the relevant targetpolypeptide antigen and multiple, for example at least three HLA class Ior at least three HLA class II molecules capable of binding to thebestEPI in at least or more than 1%, 2%, 5%, 10%, 12%, 15%, 16%, 17%,18%, 19%, 20%, 21%, 22%, 23%, 24%, 25%, 26%, 27%, 28%, 29%, 30%, 31%,32%, 33%, 34%, 35%, 36%, 37%, 38%, 39%, 40%, 41%, 42%, 43%, 44%, 45%,46%, 47%, 48%, 49% or 50% of the relevant population of human subjects.

In some cases multiple T cell epitopes/PEPI3+s, optionally from one ormore target polypeptide antigens may be ranked by the percentage ofsubjects in the model or intend-to-treat population having multiple, forexample at least three HLA class I or at least three HLA class IImolecules capable of binding to each fragment; or by the percentage ofsubjects in the model or intend-to-treat population that are predictedto express both the target polypeptide antigen comprising the fragmentand multiple, for example at least three HLA class I or at least threeHLA class II molecules capable of binding to the fragments. The peptideor composition may be designed to comprise one or more PEPI3+s that areselected based on their ranking.

Typically each bestEPI is a fragment of a target polypeptide antigen andpolypeptides that comprise one or more of the bestEPIs are the targetpolypeptide antigens for the treatment, vaccination or immunotherapy.The method may comprise the step of identifying one or more suitabletarget polypeptide antigens. Typically each target polypeptide antigenwill be associated with the same disease or condition, pathogenicorganism or group of pathogenic organisms or virus, or type of cancer.

The composition, kit or panel may comprise, or the method may compriseselecting, for each bestEPI a sequence of up to 50, 45, 40, 35, 30, 25,20, 19, 18, 17, 16, 15, 14, 13, 12, 11, 10 or 9 consecutive amino acidsof the target polypeptide antigen, such as a polypeptide describedherein, which consecutive amino acids comprise the amino acid sequenceof the bestEPI.

In some cases the amino acid sequence is flanked at the N and/or Cterminus by additional amino acids that are not part of the consecutivesequence of the target polypeptide antigen. In some cases the sequenceis flanked by up to 41 or 35 or 30 or 25 or 20 or 15 or 10, or 9 or 8 or7 or 6 or 5 or 4 or 3 or 2 or 1 additional amino acid at the N and/or Cterminus or between target polypeptide fragments. In other cases eachpolypeptide either consists of a fragment of a target polypeptideantigen, or consists of two or more such fragments arranged end to end(arranged sequentially in the peptide end to end) or overlapping in asingle peptide (where two or more of the fragments comprise partiallyoverlapping sequences, for example where two bestEPIs in the samepolypeptide are within 50 amino acids of each other).

When fragments of different polypeptides or from different regions ofthe same polypeptide are joined together in an engineered peptide thereis the potential for neoepitopes to be generated around the join orjunction. Such neoepitopes encompass at least one amino acid from eachfragment on either side of the join or junction, and may be referred toherein as junctional amino acid sequences. The neoepitopes may induceundesired T cell responses against healthy cells (autoimmunity). Thepeptides may be designed, or the polypeptides may be screened, to avoid,eliminate or minimise neoepitopes that correspond to a fragment of aprotein expressed in normal healthy human cells and/or neoepitopes thatare capable of binding to at least two, or in some cases at least three,or at least four HLA class I molecules of the subject, or in some casesat least two, or at least three or four or five HLA class II moleculesof the subject. In some cases the peptide is designed, or thepolypeptide screened, to eliminate polypeptides having a junctionalneoepitope that is capable of binding in more than a thresholdpercentage of human subjects in a specific, target or model population,to at least two HLA class I molecules expressed by individual subjectsof the population. In some cases the threshold is 30%, or 20%, or 15%,or 10%, or 5%, or 2%, or 1%, or 0.5% of said population. The methods ofthe disclosure may be used to identify or screen for such neoepitopes asdescribed herein. Alignment may be determined using known methods suchas BLAST algorithms. Software for performing BLAST analyses is publiclyavailable through the National Center for Biotechnology Information(ncbi.nlm.nih.gov/).

The at least two bestEPIs of the composition polypeptides may bothtarget a single antigen (e.g a polypeptide vaccine comprising twomultiple HLA-binding PEPIs derived from a single antigen, for example atumor associated antigen, targeted by the vaccine/immunotherapy) or maytarget different antigens (e.g. a polypeptide vaccine comprising onemultiple HLA-binding PEPI derived from one antigen, e.g. a tumorassociated antigen, and a second multiple HLA-binding PEPI derived froma different antigen, e.g. a different tumor associated antigen, bothtargeted by the vaccine/immunotherapy).

In some cases the active ingredient polypeptide(s) together comprise, orthe method comprises selecting, a total of or at least 2, 3, 4, 5, 6, 7,8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24 25, 26,27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39 or 40 or moredifferent bestEPIs. The bestEPIs may be fragments of one or moredifferent target polypeptide antigens. By identifying the specificfragments of each target polypeptide antigen that are immunogenic for ahigh proportion of subjects in a target population it is possible toincorporate multiple such fragments, optionally from multiple differenttarget polypeptide antigens, in a single active ingredient polypeptideor multiple active ingredient polypeptides intended for use incombination or to maximise the number of T cell clones that can beactivated by one or more polypeptides of a certain length.

Currently most vaccines and immunotherapy compositions target only asingle polypeptide antigen. However according to the present disclosureit is in some cases beneficial to provide a pharmaceutical compositionor an active ingredient polypeptide that targets two or more differentpolypeptide antigens. For example, most cancers or tumors areheterogeneous, meaning that different cancer or tumor cells of a subject(over-)express different antigens. The tumour cells of different cancerpatients also express different combinations of tumour-associatedantigens. The anti-cancer immunogenic compositions that are most likelyto be effective are those that target multiple antigens expressed by thetumor, and therefore more cancer or tumor cells, in an individual humansubject or in a population.

The beneficial effect of combining multiple bestEPIs in a singletreatment (administration of one or more pharmaceutical compositionsthat together comprise multiple PEPIs), can be illustrated by thepersonalised vaccine polypeptides described in Examples 15 and 16 below.Exemplary CTA expression probabilities in ovarian cancer are as follows:BAGE: 30%; MAGE A9: 37%; MAGE A4: 34%; MAGE A10: 52%. If patient XYZwere treated with a vaccine comprising PEPIs in only BAGE and MAGE A9,then the probability of having a mAGP (multiple expressed antigens withPEPI) would be 11%. If patent XYZ were treated with a vaccine comprisingonly PEPIs for the MAGE A4 and MAGE A10 CTAs, then the probability ofhaving a multiAGP would be 19%. However if a vaccine contained all 4 ofthese CTAs (BAGE, MAGE A9, MAGE A4 and MAGE A10), then the probabilityof having a mAGP would be 50%. In other words the effect would begreater than the combined probabilities of mAGP for both two-PEPItreatments (probability mAGP for BAGE/MAGE+ probability mAGP for MAGE A4and MAGE A10). Patient XYZ's PIT vaccine described in Example 15contains a further 9 PEPIs, and thus, the probability of having a mAGPis over 99.95%.

Likewise exemplary CTA expression probabilities in breast cancer are asfollows: MAGE C2: 21%; MAGE A1: 37%; SPC1: 38%; MAGE A9: 44%. Treatmentof patient ABC with a vaccine comprising PEPIs in only MAGE C2: 21% andMAGE A1 has a mAGP probability of 7%. Treatment of patient ABC with avaccine comprising PEPIs in only SPC1: 38%; MAGE A9 has a mAGPprobability of 11%. Treatment of patient ABC with a vaccine comprisingPEPIs in MAGE C2: 21%; MAGE A1: 37%; SPC1: 38%; MAGE A9 has a mAGPprobability of 44% (44>7+11). Patient ABC's PIT vaccine described inExample 16 contains a further 8 PEPIs, and thus, the probability ofhaving a mAGP is over 99.93%.

Accordingly in some cases the bestEPIs of the active ingredientpolypeptides are from two or more different target polypeptide antigens,for example different antigens associated with a specific disease orcondition, for example different cancer- or tumor-associated antigens orantigens expressed by a target pathogen. In some cases the PEPIs arefrom a total of or at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14,15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32,33, 34, 35, 36, 37, 38, 39 or 40 or more different target polypeptideantigens. The different target polypeptide antigens may be any differentpolypeptides that it is useful to target or that can be selectivelytargeted with different PEPI3+s. In some cases different targetpolypeptide antigens are non-homologues or non-paralogues or have lessthan 95%, or 90%, or 85% or 80% or 75% or 70% or 60% or 50% sequenceidentity across the full length of each polypeptide. In some casesdifferent polypeptides are those that do not share any PEPI3+s.Alternatively, in some cases the PEPI3+s are from different targetpolypeptide antigens when they are not shared with other polypeptideantigens targeted by the active ingredient polypeptides.

In some cases one or more or each of the immunogenic polypeptidefragments is from a polypeptide that is present in a sample taken from ahuman subject (e.g., of the target population). This indicates that thepolypeptide is expressed in the subject, for example a cancer- ortumor-associated antigen or a cancer testis antigen expressed by cancercells of the subject. In some cases one or more or each of thepolypeptides is a mutational neoantigen, or an expressional neoantigenof the subject. One or more or each fragment may comprise a neoantigenspecific mutation.

In other cases one or more or each of the immunogenic polypeptidefragments is from a target polypeptide antigen that is not generallyexpressed or is minimally expressed in normal healthy cells or tissue,but is expressed in a high proportion of (with a high frequency in)subjects or in the diseased cells of a subject having a particulardisease or condition, as described above. The method my compriseidentifying or selecting such a target polypeptide antigen. In somecases two or more or each of the immunogenic polypeptidefragments/bestEPIs are from different cancer- or tumor-associatedantigens that are each (over-)expressed with a high frequency insubjects having a type of cancer or a cancer derived from a particularcell type or tissue. In some cases the immunogenic polypeptide fragmentsare from a total of or at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12,13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30,31, 32, 33, 34, 35, 36, 37, 38, 39 or 40 different cancer- ortumor-associated polypeptides. In some cases one or more or each or atleast one, at least two, at least three, at least four, at least five orat least six or at least seven of the polypeptides are selected from theantigens listed in any one of Tables 2 to 7.

In some cases one or more or each of the target polypeptide antigens isa cancer testis antigen (CTA). In some cases the immunogenic polypeptidefragments/bestEPIs are from at least 1, or at least 2, 3, 4, 5, 6, 7, 8,9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24 or 25CTAs, or from a total of 3 or more different target polypeptideantigens, optionally wherein 1, 2, or all three or at least three areCTAs, or from 4 or more different polypeptide antigens, optionallywherein 1, 2, 3 or all four or at least 1, 2, 3 or 4 are CTAs, or from 5or more different polypeptide antigens, optionally wherein 1, 2, 3, 4 orall five or at least 1, 2, 3, 4, or 5 are CTAs, or from 6 or moredifferent polypeptide antigens, optionally wherein 1, 2, 3, 4, 5 or allsix or at least 1, 2, 3, 4, 5, or 6 are CTAs, or from 7 or moredifferent polypeptide antigens, optionally wherein 1, 2, 3, 4, 5, 6 orall 7 or at least 1, 2, 3, 4, 5, 6 or 7 are CTAs, or from 8 or moredifferent polypeptide antigens, optionally wherein 1, 2, 3, 4, 5, 6, 7or all 8 or at least 1, 2, 3, 4, 5, 6, 7 or 8 are CTAs. In some casesone or more or each of the target polypeptide antigens is expressed by abacteria, a virus, or a parasite.

In some cases one or more of the polypeptide fragments comprises anamino acid sequence that is a T cell epitope capable of binding to atleast two, or at least three HLA class I of a high percentage ofsubjects in the population subject and one or more of the polypeptidefragments comprises an amino acid sequence that is a T cell epitopecapable of binding to at least two, or at least three, or at least fourHLA class II of the subject of a high percentage of subjects in thepopulation, wherein the HLA class I and HLA class II binding fragmentsmay optionally overlap. A composition prepared by such a method mayelicit both a cytotoxic T cell response and a helper T cell response inthe subject.

Immunogenic and Pharmaceutical Compositions, Methods of Treatment andModes of Administration

In some aspects the disclosure relates to a pharmaceutical composition,kit, or panels of polypeptides as described above having one or morepolypeptides as active ingredient(s). These may be for use in a methodof inducing an immune response, treating, vaccinating or providingimmunotherapy to a subject, and the pharmaceutical composition may be avaccine or immunotherapy composition. Such a treatment comprisesadministering one or more polypeptides or pharmaceutical compositionsthat together comprise all of the active ingredient polypeptides of thetreatment to the subject. Multiple polypeptides or pharmaceuticalcompositions may be administered together or sequentially, for exampleall of the pharmaceutical compositions or polypeptides may beadministered to the subject within a period of 1 year, or 6 months, or 3months, or 60 or 50 or 40 or 30 days.

The immunogenic or pharmaceutical compositions or kits described hereinmay comprise, in addition to one or more immunogenic peptides, apharmaceutically acceptable excipient, carrier, diluent, buffer,stabiliser, preservative, adjuvant or other materials well known tothose skilled in the art. Such materials are preferably non-toxic andpreferably do not interfere with the pharmaceutical activity of theactive ingredient(s). The pharmaceutical carrier or diluent may be, forexample, water containing solutions. The precise nature of the carrieror other material may depend on the route of administration, e.g. oral,intravenous, cutaneous or subcutaneous, nasal, intramuscular,intradermal, and intraperitoneal routes.

The pharmaceutical compositions of the disclosure may comprise one ormore “pharmaceutically acceptable carriers”. These are typically large,slowly metabolized macromolecules such as proteins, saccharides,polylactic acids, polyglycolic acids, polymeric amino acids, amino acidcopolymers, sucrose (Paoletti et al., 2001, Vaccine, 19:2118), trehalose(WO 00/56365), lactose and lipid aggregates (such as oil droplets orliposomes). Such carriers are well known to those of ordinary skill inthe art. The pharmaceutical compositions may also contain diluents, suchas water, saline, glycerol, etc. Additionally, auxiliary substances,such as wetting or emulsifying agents, pH buffering substances, and thelike, may be present. Sterile pyrogen-free, phosphate bufferedphysiologic saline is a typical carrier (Gennaro, 2000, Remington: TheScience and Practice of Pharmacy, 20th edition, ISBN:0683306472).

The pharmaceutical compositions of the disclosure may be lyophilized orin aqueous form, i.e. solutions or suspensions. Liquid formulations ofthis type allow the compositions to be administered direct from theirpackaged form, without the need for reconstitution in an aqueous medium,and are thus ideal for injection. The pharmaceutical compositions may bepresented in vials, or they may be presented in ready filled syringes.The syringes may be supplied with or without needles. A syringe willinclude a single dose, whereas a vial may include a single dose ormultiple doses.

Liquid formulations of the disclosure are also suitable forreconstituting other medicaments from a lyophilized form. Where apharmaceutical composition is to be used for such extemporaneousreconstitution, the disclosure provides a kit, which may comprise twovials, or may comprise one ready-filled syringe and one vial, with thecontents of the syringe being used to reconstitute the contents of thevial prior to injection.

The pharmaceutical compositions of the disclosure may include anantimicrobial, particularly when packaged in a multiple dose format.Antimicrobials may be used, such as 2-phenoxyethanol or parabens(methyl, ethyl, propyl parabens). Any preservative is preferably presentat low levels. Preservative may be added exogenously and/or may be acomponent of the bulk antigens which are mixed to form the composition(e.g. present as a preservative in pertussis antigens).

The pharmaceutical compositions of the disclosure may comprise detergente.g. Tween (polysorbate), DMSO (dimethyl sulfoxide), DMF(dimethylformamide). Detergents are generally present at low levels,e.g. <0.01%, but may also be used at higher levels, e.g. 0.01-50%.

The pharmaceutical compositions of the disclosure may include sodiumsalts (e.g. sodium chloride) and free phosphate ions in solution (e.g.by the use of a phosphate buffer).

In certain embodiments, the pharmaceutical composition may beencapsulated in a suitable vehicle either to deliver the peptides intoantigen presenting cells or to increase the stability. As will beappreciated by a skilled artisan, a variety of vehicles are suitable fordelivering a pharmaceutical composition of the disclosure. Non-limitingexamples of suitable structured fluid delivery systems may includenanoparticles, liposomes, microemulsions, micelles, dendrimers and otherphospholipid-containing systems. Methods of incorporating pharmaceuticalcompositions into delivery vehicles are known in the art.

In order to increase the immunogenicity of the composition, thepharmacological compositions may comprise one or more adjuvants and/orcytokines.

Suitable adjuvants include an aluminum salt such as aluminum hydroxideor aluminum phosphate, but may also be a salt of calcium, iron or zinc,or may be an insoluble suspension of acylated tyrosine, or acylatedsugars, or may be cationically or anionically derivatised saccharides,polyphosphazenes, biodegradable microspheres, monophosphoryl lipid A(MPL), lipid A derivatives (e.g. of reduced toxicity), 3-O-deacylatedMPL [3D-MPL], quil A, Saponin, QS21, Freund's Incomplete Adjuvant (DifcoLaboratories, Detroit, Mich.), Merck Adjuvant 65 (Merck and Company,Inc., Rahway, N.J.), AS-2 (Smith-Kline Beecham, Philadelphia, Pa.), CpGoligonucleotides, bioadhesives and mucoadhesives, microparticles,liposomes, polyoxyethylene ether formulations, polyoxyethylene esterformulations, muramyl peptides or imidazoquinolone compounds (e.g.imiquamod and its homologues). Human immunomodulators suitable for useas adjuvants in the disclosure include cytokines such as interleukins(e.g. IL-1, IL-2, IL-4, IL-5, IL-6, IL-7, IL-12, etc), macrophage colonystimulating factor (M-CSF), tumour necrosis factor (TNF), granulocyte,macrophage colony stimulating factor (GM-CSF) may also be used asadjuvants.

In some embodiments, the compositions comprise an adjuvant selected fromthe group consisting of Montanide ISA-51 (Seppic, Inc., Fairfield, N.J.,United States of America), QS-21 (Aquila Biopharmaceuticals, Inc.,Lexington, Mass., United States of America), GM-CSF, cyclophosamide,bacillus Calmette-Guerin (BCG), corynbacterium parvum, levamisole,azimezone, isoprinisone, dinitrochlorobenezene (DNCB), keyhole limpethemocyanins (KLH), Freunds adjuvant (complete and incomplete), mineralgels, aluminum hydroxide (Alum), lysolecithin, pluronic polyols,polyanions, oil emulsions, dinitrophenol, diphtheria toxin (DT).

By way of example, the cytokine may be selected from the groupconsisting of a transforming growth factor (TGF) such as but not limitedto TGF-α and TGF-β; insulin-like growth factor-I and/or insulin-likegrowth factor-II; erythropoietin (EPO); an osteoinductive factor; aninterferon such as but not limited to interferon-.α, -β, and -γ; acolony stimulating factor (CSF) such as but not limited tomacrophage-CSF (M-CSF); granulocyte-macrophage-CSF (GM-CSF); andgranulocyte-CSF (G-CSF). In some embodiments, the cytokine is selectedfrom the group consisting of nerve growth factors such as NGF-β;platelet-growth factor; a transforming growth factor (TGF) such as butnot limited to TGF-α. and TGF-β; insulin-like growth factor-I andinsulin-like growth factor-II; erythropoietin (EPO); an osteoinductivefactor; an interferon (IFN) such as but not limited to IFN-α, IFN-β, andIFN-γ; a colony stimulating factor (CSF) such as macrophage-CSF (M-CSF);granulocyte-macrophage-CSF (GM-CSF); and granulocyte-CSF (G-CSF); aninterleukin (I1) such as but not limited to IL-1, IL-1.alpha., IL-2,IL-3, IL-4, IL-5, IL-6, IL-7, IL-8, IL-9, IL-10, IL-11, IL-12; IL-13,IL-14, IL-15, IL-16, IL-17, IL-18; LIF; kit-ligand or FLT-3;angiostatin; thrombospondin; endostatin; a tumor necrosis factor (TNF);and LT.

It is expected that an adjuvant or cytokine can be added in an amount ofabout 0.01 mg to about 10 mg per dose, preferably in an amount of about0.2 mg to about 5 mg per dose. Alternatively, the adjuvant or cytokinemay be at a concentration of about 0.01 to 50%, preferably at aconcentration of about 2% to 30%.

In certain aspects, the pharmaceutical compositions of the disclosureare prepared by physically mixing the adjuvant and/or cytokine with thePEPIs under appropriate sterile conditions in accordance with knowntechniques to produce the final product.

Examples of suitable compositions of polypeptide fragments and methodsof administration are provided in Esseku and Adeyeye (2011) and Van denMooter G. (2006). Vaccine and immunotherapy composition preparation isgenerally described in Vaccine Design (“The subunit and adjuvantapproach” (eds Powell M. F. & Newman M. J. (1995) Plenum Press NewYork). Encapsulation within liposomes, which is also envisaged, isdescribed by Fullerton, U.S. Pat. No. 4,235,877.

In some embodiments, the compositions disclosed herein are prepared as anucleic acid vaccine. In some embodiments, the nucleic acid vaccine is aDNA vaccine. In some embodiments, DNA vaccines, or gene vaccines,comprise a plasmid with a promoter and appropriate transcription andtranslation control elements and a nucleic acid sequence encoding one ormore polypeptides of the disclosure. In some embodiments, the plasmidsalso include sequences to enhance, for example, expression levels,intracellular targeting, or proteasomal processing. In some embodiments,DNA vaccines comprise a viral vector containing a nucleic acid sequenceencoding one or more polypeptides of the disclosure. In additionalaspects, the compositions disclosed herein comprise one or more nucleicacids encoding peptides determined to have immunoreactivity with abiological sample. For example, in some embodiments, the compositionscomprise one or more nucleotide sequences encoding 1, 2, 3, 4, 5, 6, 7,8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, or more peptidescomprising a fragment that is a T cell epitope capable of binding to atleast three HLA class I molecules and/or at least three HLA class IImolecules of a patient. In some embodiments, the peptides are derivedfrom an antigen that is expressed in cancer. In some embodiments the DNAor gene vaccine also encodes immunomodulatory molecules to manipulatethe resulting immune responses, such as enhancing the potency of thevaccine, stimulating the immune system or reducing immunosuppression.Strategies for enhancing the immunogenicity of DNA or gene vaccinesinclude encoding of xenogeneic versions of antigens, fusion of antigensto molecules that activate T cells or trigger associative recognition,priming with DNA vectors followed by boosting with viral vector, andutilization of immunomodulatory molecules. In some embodiments, the DNAvaccine is introduced by a needle, a gene gun, an aerosol injector, withpatches, via microneedles, by abrasion, among other forms. In some formsthe DNA vaccine is incorporated into liposomes or other forms ofnanobodies. In some embodiments, the DNA vaccine includes a deliverysystem selected from the group consisting of a transfection agent;protamine; a protamine liposome; a polysaccharide particle; a cationicnanoemulsion; a cationic polymer; a cationic polymer liposome; acationic nanoparticle; a cationic lipid and cholesterol nanoparticle; acationic lipid, cholesterol, and PEG nanoparticle; a dendrimernanoparticle. In some embodiments, the DNA vaccines is administered byinhalation or ingestion. In some embodiments, the DNA vaccine isintroduced into the blood, the thymus, the pancreas, the skin, themuscle, a tumor, or other sites.

In some embodiments, the compositions disclosed herein are prepared asan RNA vaccine. In some embodiments, the RNA is non-replicating mRNA orvirally derived, self-amplifying RNA. In some embodiments, thenon-replicating mRNA encodes the peptides disclosed herein and contains5′ and 3′ untranslated regions (UTRs). In some embodiments, the virallyderived, self-amplifying RNA encodes not only the peptides disclosedherein but also the viral replication machinery that enablesintracellular RNA amplification and abundant protein expression. In someembodiments, the RNA is directly introduced into the individual. In someembodiments, the RNA is chemically synthesized or transcribed in vitro.In some embodiments, the mRNA is produced from a linear DNA templateusing a T7, a T3, or an Sp6 phage RNA polymerase, and the resultingproduct contains an open reading frame that encodes the peptidesdisclosed herein, flanking UTRs, a 5′ cap, and a poly(A) tail. In someembodiments, various versions of 5′ caps are added during or after thetranscription reaction using a vaccinia virus capping enzyme or byincorporating synthetic cap or anti-reverse cap analogues. In someembodiments, an optimal length of the poly(A) tail is added to mRNAeither directly from the encoding DNA template or by using poly(A)polymerase. The RNA encodes one or more peptides comprising a fragmentthat is a T cell epitope capable of binding to at least three HLA classI and/or at least three HLA class II molecules of a patient. In someembodiments, the fragments are derived from an antigen that is expressedin cancer. In some embodiments, the RNA includes signals to enhancestability and translation. In some embodiments, the RNA also includesunnatural nucleotides to increase the half-life or modified nucleosidesto change the immunostimulatory profile. In some embodiments, the RNAsis introduced by a needle, a gene gun, an aerosol injector, withpatches, via microneedles, by abrasion, among other forms. In some formsthe RNA vaccine is incorporated into liposomes or other forms ofnanobodies that facilitate cellular uptake of RNA and protect it fromdegradation. In some embodiments, the RNA vaccine includes a deliverysystem selected from the group consisting of a transfection agent;protamine; a protamine liposome; a polysaccharide particle; a cationicnanoemulsion; a cationic polymer; a cationic polymer liposome; acationic nanoparticle; a cationic lipid and cholesterol nanoparticle; acationic lipid, cholesterol, and PEG nanoparticle; a dendrimernanoparticle; and/or naked mRNA; naked mRNA with in vivoelectroporation; protamine-complexed mRNA; mRNA associated with apositively charged oil-in-water cationic nanoemulsion; mRNA associatedwith a chemically modified dendrimer and complexed with polyethyleneglycol (PEG)-lipid; protamine-complexed mRNA in a PEG-lipidnanoparticle; mRNA associated with a cationic polymer such aspoyethylenimine (PEI); mRNA associated with a cationic polymer such asPEI and a lipid component; mRNA associated with a polysaccharide (forexample, chitosan) particle or gel; mRNA in a cationic lipidnanoparticle (for example, 1,2-dioleoyloxy-3-trimethylammoniumpropane(DOTAP) or dioleoylphosphatidylethanolainine (DOPE) lipids); mRNAcomplexed with cationic lipids and cholesterol; or mRNA complexed withcationic lipids, cholesterol and PEG-lipid. In some embodiments, the RNAvaccine is administered by inhalation or ingestion. In some embodiments,the RNA is introduced into the blood, the thymus, the pancreas, theskin, the muscle, a tumor, or other sites, and/or by an intradermal,intramuscular, subcutaneous, intranasal, intranodal, intravenous,intrasplenic, intratumoral or other delivery route.

Polynucleotide or oligonucleotide components may be naked nucleotidesequences or be in combination with cationic lipids, polymers ortargeting systems. They may be delivered by any available technique. Forexample, the polynucleotide or oligonucleotide may be introduced byneedle injection, preferably intradermally, subcutaneously orintramuscularly. Alternatively, the polynucleotide or oligonucleotidemay be delivered directly across the skin using a delivery device suchas particle-mediated gene delivery. The polynucleotide oroligonucleotide may be administered topically to the skin, or to mucosalsurfaces for example by intranasal, oral, or intrarectal administration.

Uptake of polynucleotide or oligonucleotide constructs may be enhancedby several known transfection techniques, for example those includingthe use of transfection agents. Examples of these agents includecationic agents, for example, calcium phosphate and DEAE-Dextran andlipofectants, for example, lipofectam and transfectam. The dosage of thepolynucleotide or oligonucleotide to be administered can be altered.

Administration is typically in a “prophylactically effective amount” ora “therapeutically effective amount” (as the case may be, althoughprophylaxis may be considered therapy), this being sufficient to resultin a clinical response or to show clinical benefit to the individual,e.g. an effective amount to prevent or delay onset of the disease orcondition, to ameliorate one or more symptoms, to induce or prolongremission, or to delay relapse or recurrence.

The dose may be determined according to various parameters, especiallyaccording to the substance used; the age, weight and condition of theindividual to be treated; the route of administration; and the requiredregimen. The amount of antigen in each dose is selected as an amountwhich induces an immune response. A physician will be able to determinethe required route of administration and dosage for any particularindividual. The dose may be provided as a single dose or may be providedas multiple doses, for example taken at regular intervals, for example2, 3 or 4 doses administered hourly. Typically peptides, polynucleotidesor oligonucleotides are typically administered in the range of 1 pg to 1mg, more typically 1 pg to 10 μg for particle mediated delivery and 1 μgto 1 mg, more typically 1-100 μg, more typically 5-50 μg for otherroutes. Generally, it is expected that each dose will comprise 0.01-3 mgof antigen. An optimal amount for a particular vaccine can beascertained by studies involving observation of immune responses insubjects.

Examples of the techniques and protocols mentioned above can be found inRemington's Pharmaceutical Sciences, 20th Edition, 2000, pub.Lippincott, Williams & Wilkins.

In some cases in accordance with the disclosure, more than one peptideor composition of peptides is administered. Two or more pharmaceuticalcompositions may be administered together/simultaneously and/or atdifferent times or sequentially. Thus, the disclosure includes sets ofpharmaceutical compositions and uses thereof. The use of combination ofdifferent peptides, optionally targeting different antigens, isimportant to overcome the challenges of genetic heterogeneity of tumorsand HLA heterogeneity of individuals. The use of peptides of thedisclosure in combination expands the group of individuals who canexperience clinical benefit from vaccination. Multiple pharmaceuticalcompositions of PEPIs, manufactured for use in one regimen, may define adrug product.

Routes of administration include but are not limited to intranasal,oral, subcutaneous, intradermal, and intramuscular. The subcutaneousadministration is particularly preferred. Subcutaneous administrationmay for example be by injection into the abdomen, lateral and anterioraspects of upper arm or thigh, scapular area of back, or upperventrodorsal gluteal area.

The compositions of the disclosure may also be administered in one, ormore doses, as well as, by other routes of administration. For example,such other routes include, intracutaneously, intravenously,intravascularly, intraarterially, intraperitnoeally, intrathecally,intratracheally, intracardially, intralobally, intramedullarly,intrapulmonarily, and intravaginally. Depending on the desired durationof the treatment, the compositions according to the disclosure may beadministered once or several times, also intermittently, for instance ona monthly basis for several months or years and in different dosages.

Solid dosage forms for oral administration include capsules, tablets,caplets, pills, powders, pellets, and granules. In such solid dosageforms, the active ingredient is ordinarily combined with one or morepharmaceutically acceptable excipients, examples of which are detailedabove. Oral preparations may also be administered as aqueoussuspensions, elixirs, or syrups. For these, the active ingredient may becombined with various sweetening or flavoring agents, coloring agents,and, if so desired, emulsifying and/or suspending agents, as well asdiluents such as water, ethanol, glycerin, and combinations thereof.

One or more compositions of the disclosure may be administered, or themethods and uses for treatment according to the disclosure may beperformed, alone or in combination with other pharmacologicalcompositions or treatments, for example chemotherapy and/orimmunotherapy and/or vaccine. The other therapeutic compositions ortreatments may for example be one or more of those discussed herein, andmay be administered either simultaneously or sequentially with (beforeor after) the composition or treatment of the disclosure.

In some cases the treatment may be administered in combination withcheckpoint blockade therapy/checkpopint inhibitors, co-stimulatoryantibodies, cytotoxic or non-cytotoxic chemotherapy and/or radiotherapy,targeted therapy or monoclonal antibody therapy. It has beendemonstrated that chemotherapy sensitizes tumors to be killed by tumorspecific cytotoxic T cells induced by vaccination (Ramakrishnan et al. JClin Invest. 2010; 120(4):1111-1124). Examples of chemotherapy agentsinclude alkylating agents including nitrogen mustards such asmechlorethamine (HN2), cyclophosphamide, ifosfamide, melphalan(L-sarcolysin) and chlorambucil; anthracyclines; epothilones;nitrosoureas such as carmustine (BCNU), lomustine (CCNU), semustine(methyl-CCNU) and streptozocin (streptozotocin); triazenes such asdecarbazine (DTIC; dimethyltriazenoimidazole-carboxamide;ethylenimines/methylmelamines such as hexamethylmelamine, thiotepa;alkyl sulfonates such as busulfan; Antimetabolites including folic acidanalogues such as methotrexate (amethopterin); alkylating agents,antimetabolites, pyrimidine analogs such as fluorouracil(5-fluorouracil; 5-FU), floxuridine (fluorodeoxyuridine; FUdR) andcytarabine (cytosine arabinoside); purine analogues and relatedinhibitors such as mercaptopurine (6-mercaptopurine; 6-MP), thioguanine(6-thioguanine; TG) and pentostatin (2′-deoxycoformycin);epipodophylotoxins; enzymes such as L-asparaginase; biological responsemodifiers such as IFNα, IL-2, G-CSF and GM-CSF; platinum coordinationcomplexes such as cisplatin (cis-DDP), oxaliplatin and carboplatin;anthracenediones such as mitoxantrone and anthracycline; substitutedurea such as hydroxyurea; methylhydrazine derivatives includingprocarbazine (N-methylhydrazine, MIH) and procarbazine; adrenocorticalsuppressants such as mitotane (o,p′-DDD) and aminoglutethimide; taxoland analogues/derivatives; hormones/hormonal therapy andagonists/antagonists including adrenocorticosteroid antagonists such asprednisone and equivalents, dexamethasone and aminoglutethimide,progestin such as hydroxyprogesterone caproate, medroxyprogesteroneacetate and megestrol acetate, estrogen such as diethylstilbestrol andethinyl estradiol equivalents, antiestrogen such as tamoxifen, androgensincluding testosterone propionate and fluoxymesterone/equivalents,antiandrogens such as flutamide, gonadotropin-releasing hormone analogsand leuprolide and non-steroidal antiandrogens such as flutamide;natural products including vinca alkaloids such as vinblastine (VLB) andvincristine, epipodophyllotoxins such as etoposide and teniposide,antibiotics such as dactinomycin (actinomycin D), daunorubicin(daunomycin; rubidomycin), doxorubicin, bleomycin, plicamycin(mithramycin) and mitomycin (mitomycin C), enzymes such asL-asparaginase, and biological response modifiers such as interferonalphenomes.

In some cases the method of treatment is a method of vaccination or amethod of providing immunotherapy. As used herein, “immunotherapy” isthe treatment of a disease or condition by inducing or enhancing animmune response in an individual. In certain embodiments, immunotherapyrefers to a therapy that comprises the administration of one or moredrugs to an individual to elicit T cell responses. In a specificembodiment, immunotherapy refers to a therapy that comprises theadministration or expression of polypeptides that contain one or morePEPIs to an individual to elicit a T cell response to recognize and killcells that display the one or more PEPIs on their cell surface inconjunction with a class I HLA. In another specific embodiment,immunotherapy comprises the administration of one or more PEPIs to anindividual to elicit a cytotoxic T cell response against cells thatdisplay tumor associated antigens (TAAs) or cancer testis antigens(CTAs) comprising the one or more PEPIs on their cell surface. Inanother embodiment, immunotherapy refers to a therapy that comprises theadministration or expression of polypeptides that contain one or morePEPIs presented by class II HLAs to an individual to elicit a T helperresponse to provide co-stimulation to cytotoxic T cells that recognizeand kill diseased cells that display the one or more PEPIs on their cellsurface in conjunction with a class I HLAs. In still another specificembodiment, immunotherapy refers to a therapy that comprisesadministration of one or more drugs to an individual that re-activateexisting T cells to kill target cells. The theory is that the cytotoxicT cell response will eliminate the cells displaying the one or morePEPIs, thereby improving the clinical condition of the individual. Insome instances, immunotherapy may be used to treat tumors. In otherinstances, immunotherapy may be used to treat intracellularpathogen-based diseases or disorders.

In some cases the disclosure relates to the treatment of cancer or thetreatment of solid tumors. The treatment may be of cancers or malignantor benign tumors of any cell, tissue, or organ type. The cancer may ormay not be metastatic. Exemplary cancers include carcinomas, sarcomas,lymphomas, leukemias, germ cell tumors, or blastomas. The cancer may ormay not be a hormone related or dependent cancer (e.g., an estrogen orandrogen related cancer).

In other cases the disclosure relates to the treatment of a viral,bacterial, fungal or parasitic infection, or any other disease orcondition that may be treated by immunotherapy.

Systems

The disclosure provides a system comprising a storage module configuredto store data comprising the class I and/or class II HLA genotypes ofeach subject of a model population of human subjects; and the amino acidsequence of one or more test polypeptides; wherein the model populationis representative of a test target human population; and a computationmodule configured to identify and/or quantify the amino acid sequencesin the one or more test polypeptides that are capable of binding tomultiple class I HLA molecules of each subject in the model populationand/or the amino acid sequences in the one or more test polypeptidesthat are capable of binding to multiple class II HLA molecules of eachsubject in the model population. The system may further comprise anoutput module configured to display any output prediction or treatmentselection or recommendation described herein or the value of anypharmodynamic biomarker described herein.

Further Embodiments of the Disclosure

1. A method of predicting the cytotoxic T cell response rate and/or thehelper T cell response rate of a specific or target human population toadministration of a polypeptide, or to administration of apharmaceutical composition, kit or panel of polypeptides comprising oneor more polypeptides as active ingredients, the method comprising

-   -   (i) selecting or defining a relevant model human population        comprising a plurality of subjects each defined by HLA class I        genotype and/or HLA class II genotype;    -   (ii) determining for each subject in the model human population        whether the polypeptide or polypeptides together comprise        -   (a) at least one amino acid sequence that is a T cell            epitope capable of binding to at least two HLA class I            molecules of the subject; and/or        -   (b) at least one amino acid sequence that is a T cell            epitope capable of binding to at least two HLA class II            molecules of the subject; and    -   (iii) predicting        -   A. the cytotoxic T cell response rate of said human            population, wherein a higher proportion of the model human            population meeting the requirements of step (ii)(a) predicts            a higher cytotoxic T cell response rate in said human            population; and/or        -   B. the helper T cell response rate of said human population,            wherein a higher proportion of the model human population            meeting the requirements of step (ii)(b) predicts a higher            helper T cell response rate in said human population.

2. A method of predicting the clinical response rate of a specific ortarget human population to administration of a pharmaceuticalcomposition, kit or panel of polypeptides comprising one or morepolypeptides as active ingredients, the method comprising

-   -   (i) selecting or defining a relevant model human population        comprising a plurality of subjects each defined by HLA class I        genotype;    -   (ii) determining        -   (a) for each subject in the model human population whether            the one or more active ingredient polypeptides together            comprise at least two different amino acid sequences each of            which is a T cell epitope capable of binding to at least two            HLA class I molecules of the subject, optionally wherein the            at least two different amino acid sequences are comprised in            the amino acid sequence of two different polypeptide            antigens targeted by the active ingredient polypeptide(s);        -   (b) in the model population the mean number of target            polypeptide antigens that comprise at least one amino acid            sequence that is            -   A. a T cell epitope capable of binding to at least three                HLA class I molecules of the individual subjects of the                model population; and            -   B. comprised in the amino acid sequence of the active                ingredient polypeptide(s); and/or        -   (c) in the model population the mean number of expressed            target polypeptide antigens that comprise at least one amino            acid sequence that is            -   A. a T cell epitope capable of binding to at least three                HLA class I molecules of the individual subjects of the                model population; and            -   B. comprised in the amino acid sequence of the active                ingredient polypeptide(s); and    -   (iii) predicting the clinical response rate of said human        population, wherein a higher proportion of the model human        population meeting the requirements of step (ii)(a), or a higher        mean number of target polypeptides in step (ii)(b), or a higher        mean number of expressed target polypeptides in step (ii)(c)        predicts a higher clinical response rate in said human        population.

3. The method of item 1 or item 2 further comprising repeating themethod for one or more further polypeptides, pharmaceuticalcompositions, kits or panels of polypeptides, and ranking thepolypeptides, pharmaceutical compositions, kits or panels ofpolypeptides according to their predicted cytotoxic T cell, helper Tcell and/or clinical response rates in said specific or target humanpopulation.

4. The method of any one of items 1 to 3 further comprising selecting orrecommending treatment of a subject in need thereof by administration ofone or more polypeptides or pharmaceutical compositions or thepolypeptides of one or more kits or panels of polypeptides, based ontheir predicted response rate or response rate ranking.

5. The method of item 4, wherein

-   -   (a) a polypeptide, pharmaceutical composition, kit or panel of        polypeptides having a high predicted response rate or response        rate ranking is selected or recommended for inducing a        therapeutic immune response in the subject; or    -   (b) a polypeptide, pharmaceutical composition, kit or panel of        polypeptides having a low predicted response rate or response        rate ranking is selected or recommended for avoiding a toxic        immune response.

6. The method of item 4 or item 5 further comprising administering oneor more of the selected or recommended polypeptides or pharmaceuticalcompositions or the polypeptides of one or more kits or panels ofpolypeptides to the subject.

7. A method of treatment of a human subject in need thereof, the methodcomprising administering to the subject one or more polypeptides orpharmaceutical compositions that have been selected or recommended fortreatment of the subject using a method according to item 4 or item 5.

8. A method of designing or preparing a polypeptide, or a polynucleicacid that encodes a polypeptide, for use in a method of inducing animmune response in a subject of a specific or target human population,the method comprising

-   -   (i) selecting or defining        -   (a) a relevant model human population comprising a plurality            of subjects each defined by HLA class I genotype and/or by            HLA class II genotype; or        -   (b) one relevant model human population comprising a            plurality of subjects each defined by HLA class I genotype            and one relevant model human population comprising a            plurality of subjects each defined by HLA class II genotype;    -   (ii) identifying a fragment of up to 50 consecutive amino acids        of a target polypeptide antigen that comprises or consists of        -   A. a T cell epitope capable, in a high percentage of the            subjects of a model population selected or defined in            step (i) that is defined by HLA class I genotype, of binding            to at least three HLA class I molecules of the individual            subjects;        -   B. a T cell epitope capable, in a high percentage of the            subjects of a model population selected or defined in            step (i) that is defined by HLA class II genotype, of            binding to at least three HLA class II molecules of the            individual subjects; or        -   C. a T cell epitope capable, in a high percentage of the            subjects of a model population selected or defined in            step (i) that is defined by HLA class I genotype, of binding            to at least three HLA class I molecules of the individual            subjects and a T cell epitope capable, in a high percentage            of the subjects of a model population selected or defined in            step (i) that is defined by HLA class II genotype, of            binding to at least three HLA class II molecules of the            individual subjects;    -   (iii) if the polypeptide fragment selected in step (ii) is an        HLA class I—binding epitope, optionally selecting a longer        fragment of the target polypeptide antigen, which longer        fragment comprises or consists of an amino acid sequence that        -   A. comprises the fragment selected in step (ii); and        -   B. is an HLA class II molecule-binding T cell epitope            capable, in a high percentage of the subjects of a model            population selected or defined in step (i) that is defined            by HLA class II genotype, of binding to at least three, or            the most possible HLA class II molecules of the individual            subjects; and    -   (iv) designing or preparing a polypeptide, or a polynucleic acid        that encodes a polypeptide that comprises one or more        polypeptide fragments identified in step (ii) or step (iii),        optionally wherein the polypeptide fragment is flanked at the N        and/or C terminus by additional amino acids that are not part of        the sequence of the target polypeptide antigen.

9. The method of item 8, comprising identifying one or more furtherfragments of the same or one or more different target polypeptideantigens, wherein each polypeptide fragment is a T cell epitope capableof binding to at least three HLA class I molecules or at least three HLAclass II molecules of at least one subject in the model population; andranking the fragments by

-   -   (i) the percentage of subjects in the model population that        express at least three HLA class I molecules capable of binding        to the fragment;    -   (ii) the percentage of subjects in the model population that are        predicted to express both the target polypeptide antigen        comprising the fragment and at least three HLA class I molecules        capable of binding to the fragment;    -   (iii) the percentage of subjects in the model population that        express at least three HLA class II molecules capable of binding        to the fragment;    -   (iv) the percentage of subjects in the model population that are        predicted to express both the target polypeptide antigen        comprising the fragment and at least three HLA class II        molecules capable of binding to the fragment;    -   (v) the percentage of subjects in the model population that        express at least three HLA class I molecules and at least three        HLA class II molecules capable of binding to the fragment; or    -   (iv) the percentage of subjects in the model population that are        predicted to express both the target polypeptide antigen        comprising the fragment and at least three HLA class I molecules        and at least three HLA class II molecules capable of binding to        the fragment.

10. The method of item 9, which comprises selecting one or more of thepolypeptide fragments based on their ranking, and designing or preparingthe polypeptide to comprise or the polynuceic acid to encode the one ofmore selected polypeptide fragments.

11. The method of any one of items 8 to 10, further comprising designingor preparing a polypeptide, a panel of polypeptides, or a pharmaceuticalcomposition or kit comprising one or more polypeptides as activeingredients for use in a method of inducing an immune response in asubject of the specific or target human population, wherein thepolypeptide(s) or active ingredient polypeptides comprises at least twopolypeptide fragments, optionally between 2 and 15 polypeptidefragments, selected according to the method of item 8 or item 10.

12. The method of item 11, wherein the two or more or each of thefragments are from different target polypeptide antigens, optionallydifferent target polypeptide antigens selected from the antigens listedin Tables 2 to 6 and/or different cancer associated antigens, optionallywherein one or more or each of the cancer associated antigens are CTAs.

13. The method of item 11 or item 12, wherein two or more or each of thefragments are arranged in the polypeptide end to end.

14. The method of item 13, further comprising screening all of theneoepitopes formed at the join between any two of the selectedpolypeptide fragments arranged end to end in a single polypeptide toeliminate peptides comprising a neoepitope amino acid sequence that

-   -   (i) corresponds to a fragment of a human polypeptide expressed        in healthy cells;    -   (ii) is a T cell epitope capable of binding, in more than a        threshold percentage of human subjects, to at least two HLA        class I molecules expressed by individual subjects;    -   (i) meets both requirements (i) and (ii).

15. The method of any of items 8 to 14, wherein the one or morepolypeptides have been screened to eliminate polypeptides comprising anamino acid sequence that

-   -   (i) corresponds to a fragment of a human polypeptide expressed        in healthy cells; or    -   (ii) corresponds to a fragment of a human polypeptide expressed        in healthy cells and is a T cell epitope capable of binding to        at least two HLA class I molecules of the subject.

16. A method of inducing an immune response in a subject of a specificor target human population, the method comprising designing or preparinga polypeptide, a panel of polypeptides, a polynucleic acid encoding apolypeptide, or a pharmaceutical composition or kit for use in saidspecific or target human population according to the method of any oneof items 8 to 15 and administering the polypeptide(s), polynucleic acid,pharmaceutical composition or the active ingredient polypeptides of thekit to the subject.

17. A polypeptide, panel of polypeptides, polynucleic acid,pharmaceutical composition or kit for use in a method of inducing animmune response in a subject of a specific or target human population,wherein the polypeptide, panel of polypeptides, polynucleic acid,pharmaceutical composition or kit is designed or prepared according tothe method of any one of items 8 to 16 for use in said specific ortarget human population, and wherein the composition or kit optionallycomprises at least one pharmaceutically acceptable diluent, carrier, orpreservative.

18. A pharmaceutical composition, panel of polypeptides or kit for usein a method of inducing an immune response in a subject of a specific ortarget human population, wherein the pharmaceutical composition, panelof polypeptides or kit comprises as active ingredients a first and asecond and optionally one or more additional polypeptides, wherein eachpolypeptide comprises an amino acid sequence that is a T cell epitopecapable of binding to at least three HLA class I molecules of at least10% of subjects in the specific or target population, wherein the T cellepitope of the first, second and optionally any additional regions aredifferent from each other, and wherein the pharmaceutical composition orkit optionally comprises at least one pharmaceutically acceptablediluent, carrier, or preservative.

19. A pharmaceutical composition, panel of polypeptides or kit for usein a method of inducing an immune response in a human subject, whereinthe pharmaceutical composition, panel of polypeptides or kit comprisesan active ingredient polypeptide comprising a first region and a secondregion and optionally one or more additional regions, wherein eachregion comprises an amino acid sequence that is a T cell epitope capableof binding to at least three HLA class I molecules of at least 10% ofsubjects in the specific or target population, wherein the T cellepitope of the first, second and optionally any additional regions aredifferent from each other, and wherein the pharmaceutical composition orkit optionally comprises at least one pharmaceutically acceptablediluent, carrier, or preservative.

20. The pharmaceutical composition, panel of polypeptides or kit for useof item 18 or 19, wherein the amino acid sequence of one or more or eachof the T cell epitopes is from a polypeptide selected from the antigenslisted in Tables 2 to 6, or is a cancer associated antigen, optionallywherein one or more or each of the cancer associated antigens is a CTA.

21. The pharmaceutical composition, panel of polypeptides or kit for useof items 18 to 20, wherein the amino acid sequence of two or more oreach of the T cell epitopes is from a different polypeptide selectedfrom the antigens listed in Tables 2 to 6, and/or different cancerassociated antigens, optionally wherein one or more or each of thecancer associated antigens are CTAs.

22. A pharmaceutical composition, panel of polypeptides or kit for usein a method treating a cancer in a subject in need thereof, wherein thepharmaceutical composition, panel of polypeptides or kit comprises asactive ingredients a first and a second peptide and optionally one ormore additional peptides, wherein each peptide comprises an amino acidsequence that is an HLA class I-binding T cell epitope wherein at least10% of human subjects having cancer both

-   -   iii. express a tumor associated antigen selected from the        antigens listed in Table 2 that comprises said T cell epitope;        and    -   iv. have at least three HLA class I molecules capable of binding        to said T cell epitope; wherein said T cell epitope of the        first, second and optionally any additional peptides are        different from each other, and wherein the pharmaceutical        composition or kit optionally comprises at least one        pharmaceutically acceptable diluent, carrier, or preservative.

23. A pharmaceutical composition, panel of polypeptides or kit for usein a method treating a cancer in a subject in need thereof, wherein thepharmaceutical composition, panel of polypeptides or kit comprises anactive ingredient polypeptide comprising a first and a second region andoptionally one or more additional regions, wherein each region comprisesan amino acid sequence that is an HLA class I-binding T cell epitopewherein at least 10% of human subjects having cancer both

-   -   (a) express a tumor associated antigen selected from the        antigens listed in Table 2 that comprises said T cell epitope;        and    -   (b) have at least three HLA class I molecules capable of binding        to said T cell epitope; wherein said T cell epitope of the        first, second and optionally any additional regions are        different from each other, and wherein the pharmaceutical        composition or kit optionally comprises at least one        pharmaceutically acceptable diluent, carrier, or preservative.

24. A pharmaceutical composition, panel of polypeptides or kit for usein a method treating a cancer selected from colorectal, breast, ovarian,melanoma, non-melanoma skin, lung, prostate, kidney, bladder, stomach,liver, cervix uteri, oesophagus, non-Hodgkin lymphoma, leukemia,pancreas, corpus uteri, lip, oral cavity, thyroid, brain, nervoussystem, gallbladder, larynx, pharynx, myeloma, nasopharynx, Hodgkinlymphoma, testis and Kaposi sarcoma in a subject in need thereof,wherein the pharmaceutical composition, panel of polypeptides or kitcomprises as active ingredients a first and a second polypeptide andoptionally one or more additional polypeptides, wherein each polypeptidecomprises an amino acid sequence that is an HLA class I-binding T cellepitope wherein at least 10% of human subjects having said cancer both

-   -   (a) express a tumor associated antigen selected from the        antigens listed in Table 2 that comprises said T cell epitope;        and    -   (b) have at least three HLA class I molecules capable of binding        to said T cell epitope; wherein said T cell epitope of the        first, second and optionally any additional peptides are        different from each other, and wherein the pharmaceutical        composition or kit optionally comprises at least one        pharmaceutically acceptable diluent, carrier, or preservative.

25. A pharmaceutical composition, panel of polypeptides or kit for usein a method treating a cancer selected from colorectal, breast, ovarian,melanoma, non-melanoma skin, lung, prostate, kidney, bladder, stomach,liver, cervix uteri, oesophagus, non-Hodgkin lymphoma, leukemia,pancreas, corpus uteri, lip, oral cavity, thyroid, brain, nervoussystem, gallbladder, larynx, pharynx, myeloma, nasopharynx, Hodgkinlymphoma, testis and Kaposi sarcoma in a subject in need thereof,wherein the pharmaceutical composition, panel of polypeptides or kitcomprises an active ingredient polypeptide comprising a first and asecond region and optionally one or more additional regions, whereineach region comprises an amino acid sequence that is an HLA classI-binding T cell epitope wherein at least 10% of human subjects havingsaid cancer both

-   -   (a) express a tumor associated antigen selected from the        antigens listed in Table 2 that comprises said T cell epitope;        and    -   (b) have at least three HLA class I molecules capable of binding        to said T cell epitope; wherein said T cell epitope of the        first, second and optionally any additional polypeptides are        different from each other, and wherein the pharmaceutical        composition or kit optionally comprises at least one        pharmaceutically acceptable diluent, carrier, or preservative.

26. A method of treatment of a human subject in need thereof, the methodcomprising administering to the subject a polypeptide, a panel ofpolypeptides, a pharmaceutical composition or the active ingredientpolypeptides of a kit according to any one of items 17 to 25, whereinthe subject has been determined to express at least three HLA class Imolecules and/or at least three HLA class II molecules capable ofbinding to the polypeptide or to one or more of the active ingredientpoypeptides of the pharmaceutical composition or kit.

27. The method of item 26, wherein the subject has been determined toexpress at least three HLA class I and/or at least three HLA class IImolecules capable of binding to a threshold minimal number of differentT cell epitopes of the polypeptide, or the active ingredient poypeptidesof the pharmaceutical composition or kit.

28. The method of item 26 or item 27 wherein the active ingredientpolypeptides of the pharmaceutical composition, kit or panel ofpolypeptides have been determined to together comprise at least twodifferent sequences each of which is a T cell epitope capable of bindingto at least three HLA class I molecules of the subject, optionallywherein the at least two different amino acid sequences are comprised inthe amino acid sequence of two different polypeptide antigens targetedby the active ingredient polypeptide(s).

29. The method of any one or items 26 to 28 wherein the pharmaceuticalcomposition has been determined to have higher than a threshold minimumlikelihood of inducing a clinical response in the subject, wherein oneor more of the following factors corresponds to a higher likelihood ofclinical response:

-   -   (a) presence in the active ingredient polypeptide(s) of a higher        number of amino acid sequences and/or different amino acid        sequences that are each a T cell epitope capable of binding to        at least three HLA class I of the subject;    -   (b) a higher number of target polypeptide antigens, comprising        at least one amino acid sequence that is both        -   A. comprised in an active ingredient polypeptide; and        -   B. a T cell epitope capable of binding to at least three HLA            class I of the subject; optionally wherein the target            polypeptide antigens are expressed in the subject, further            optionally wherein the target polypeptides antigens are in            one or more samples obtained from the subject;    -   (c) a higher probability that the subject expresses target        polypeptide antigens, optionally a threshold number of the        target polypeptide antigens and/or optionally target polypeptide        antigens that have been determined to comprise at least one        amino acid sequence that is both        -   A. comprised in in an active ingredient polypeptide; and        -   B. a T cell epitope capable of binding to at least three HLA            class I of the subject; and/or    -   (d) a higher number of target polypeptide antigens that the        subject is predicted to express, optionally a higher number of        target polypeptide antigens that the subject expresses with a        threshold probability, and/or optionally the target polypeptide        antigens that have been determined to comprise at least one        amino acid sequence that is both        -   A. comprised in in an active ingredient polypeptide; and        -   B. a T cell epitope capable of binding to at least three HLA            class I of the subject.

30. The method of item 29, wherein the likelihood of a clinical responsehas been determined by a method comprising

-   -   (i) identifying which polypeptide antigens targeted by the        active ingredient polypeptide(s) comprise an amino acid sequence        that is both        -   A. comprised in in an active ingredient polypeptide; and        -   B. a T cell epitope capable of binding to at least three HLA            class I of the subject; (ii) using population expression            data for each antigen identified in step (i) to determine            the probability that the subject expresses one or more of            the antigens identified in step (i) that together comprise            at least two different amino acid sequences of step (i); and    -   (iii) determining the likelihood that the subject will have a        clinical response to administration of the administration of the        pharmaceutical composition, kit or panel of polypeptides,        wherein a higher probability determined in step (ii) corresponds        to a more likely clinical response.

31. A system comprising

-   -   (a) a storage module configured to store data comprising the        class I and/or class II HLA genotypes of each subject of a model        population of human subjects; and the amino acid sequence of one        or more test polypeptides; wherein the model population is        representative of a test target human population; and    -   (b) a computation module configured to identify and/or quantify        the amino acid sequences in the one or more test polypeptides        that are capable of binding to multiple class I HLA molecules of        each subject in the model population and/or the amino acid        sequences in the one or more test polypeptides that are capable        of binding to multiple class II HLA molecules of each subject in        the model population.

32. The system of item 31 further comprising

-   -   (c) an output module configured to display        -   (i) a prediction of the cytotoxic T cell response rate            and/or the helper T cell response rate of the test target            human population to administration of the one or more            polypeptides, or one or more pharmaceutical compositions            comprising the one or more polypeptides as active            ingredients; or        -   (ii) a prediction of the clinical response rate of the test            target human population to a method of treatment comprising            administration of one or more pharmaceutical compositions            comprising the one or more polypeptides as active            ingredients.

EXAMPLES Example 1—HLA-Epitope Binding Prediction Process and Validation

Predicted binding between particular HLA and epitopes (9 mer peptides)was based on the Immune Epitope Database tool for epitope prediction(iedb.org).

The HLA I-epitope binding prediction process was validated by comparisonwith HLA I-epitope pairs determined by laboratory experiments. A datasetwas compiled of HLA I-epitope pairs reported in peer reviewedpublications or public immunological databases.

The rate of agreement with the experimentally determined dataset (Table9) was determined. The binding HLA I-epitope pairs of the dataset werecorrectly predicted with a 93% probability. Coincidentally thenon-binding HLA I-epitope pairs were also correctly predicted with a 93%probability.

TABLE 9 Analytical specificity and sensitivity of the HLA-epitopebinding prediction process. HLA-epitope True epitopes (n = 327) Falseepitopes (n = 100) pairs (Binder match) (Non-binder match) HIV  91% (32) 82% (14) Viral 100% (35) 100% (11) Tumor   90% (172)  94% (32) Other(fungi, 100% (65)  95% (36) bacteria, etc.) All  93% (304)  93% (93)

The accuracy of the prediction of multiple HLA binding epitopes wasdetermined. Based on the analytical specificity and sensitivity usingthe 93% probability for both true positive and true negative predictionand 7% (=100%-93%) probability for false positive and false negativeprediction, the probability of the existence of a multiple HLA bindingepitope in a person can be calculated. The probability of multiple HLAbinding to an epitope shows the relationship between the number of HLAsbinding an epitope and the expected minimum number of real binding. PerPEPI definition three is the expected minimum number of HLA to bind anepitope (bold).

TABLE 10 Accuracy of multiple HLA binding epitopes predictions. Expectedminimum number of real Predicted number of HLAs binding to an epitopeHLA binding 0 1 2 3 4 5 6 1 35% 95% 100% 100% 100% 100% 100% 2  6% 29% 90%  99% 100% 100% 100% 3  1%  4%  22%  84%  98% 100% 100% 4  0%  0% 2%  16%  78%  96%  99% 5  0%  0%  0%  1%  10%  71%  94% 6  0%  0%  0% 0%  0%  5%  65%

The validated HLA-epitope binding prediction process was used todetermine all HLA-epitope binding pairs described in the Examples below.

Example 2—Epitope Presentation by Multiple HLA Predicts Cytotoxic TLymphocyte (CTL) Response

The presentation of one or more epitopes of a polypeptide antigen by oneor more HLA I of an individual is predictive for a CTL response wasdetermined.

The study was carried out by retrospective analysis of six clinicaltrials, conducted on 71 cancer and 9 HIV-infected patients (Table11)¹⁻⁷. Patients from these studies were treated with an HPV vaccine,three different NY-ESO-1 specific cancer vaccines, one HIV-1 vaccine anda CTLA-4 specific monoclonal antibody (Ipilimumab) that was shown toreactivate CTLs against NY-ESO-1 antigen in melanoma patients. All ofthese clinical trials measured antigen specific CD8+ CTL responses(immunogenicity) in the study subjects after vaccination. In some cases,correlation between CTL responses and clinical responses were reported.

No patient was excluded from the retroactive study for any reason otherthan data availability. The 157 patient datasets (Table 11) wererandomized with a standard random number generator to create twoindependent cohorts for training and evaluation studies. In some casesthe cohorts contained multiple datasets from the same patient, resultingin a training cohort of 76 datasets from 48 patients and atest/validation cohort of 81 datasets from 51 patients.

TABLE 11 Summary of patient datasets Immunoassay # Data sets performedin HLA Clinical Target (# antigen × the clinical genotyping trialImmunotherapy Antigen Disease # Patients* # patient) trials** method Ref1 VGX-3100 HPV16-E6 Cervical 17/18  5 × 17 IFN-γ High Resolution 1HPV16-E7 cancer ELISPOT SBT HPV18-E6 HPV18-E7 HPV16/18 2 HIVIS vaccineHIV-1 Gag AIDS  9/12 2 × 9 IFN-γ Low-Medium 2 HIV-1 RT ELISPOTResolution SSO 3 rNY-ESO-1 NY-ESO-1 Breast-and 18/18  1 × 18 In vitroand High Resolution 3 ovarian Ex vivo IFN-γ SBT 4 cancers, ELISPOTmelanoma and sarcoma 4 Ipilimumab NY-ESO-1 Metastatic 19/20  1 × 19 ICSafter T- Low to medium 5 melanoma cell resolution stimulation typing,SSP of genomic DNA, high resolution sequencing 5 NY-ESO-1f NY-ESO-1Esophageal-, 10/10  1 × 10 ICS after T- SSO probing and 6 (91-110)non-small- cell SSP of genomic cell lung- stimulation DNA and gastriccancer 6 NY-ESO-1 NY-ESO-1 Esophageal- 7/9 1 × 7 ICS after T- SSOprobing and 7 overlapping (79-173) and lung cell SSP of genomic peptidescancer, stimulation DNA malignant melanoma Total 6 7 80 157 N/A *Numberof patients used in the retrospective analysis from the original numberof patient of the clinical trials. **Immunoassays are based on T cellstimulation with antigen-specific peptide pools and quantify thereleased cytokines by different techniques. CT: Clinical trial; SBT:Sequence Based Typing; SSO: Sequence-Specific Oligonucleotide; ICS:Intracellular cytokine staining; SSP: Sequence-specific priming

The reported CTL responses of the training dataset were compared withthe HLA I restriction profile of epitopes (9 mers) of the vaccineantigens. The antigen sequences and the HLA I genotype of each patientwere obtained from publicly available protein sequence databases or peerreviewed publications and the HLA I-epitope binding prediction processwas blinded to patients' clinical CTL response data. The number ofepitopes from each antigen predicted to bind to at least 1 (PEPI1+), orat least 2 (PEPI2+), or at least 3 (PEPI3+), or at least 4 (PEPI4+), orat least 5 (PEPI5+), or all 6 (PEPI6) HLA class I molecules of eachpatient was determined and the number of HLA bound were used asclassifiers for the reported CTL responses. The true positive rate(sensitivity) and true negative rate (specificity) were determined fromthe training dataset for each classifier (number of HLA bound)separately.

ROC analysis was performed for each classifier. In a ROC curve, the truepositive rate (Sensitivity) was plotted in function of the falsepositive rate (1-Specificity) for different cut-off points (FIG. 1).Each point on the ROC curve represents a sensitivity/specificity paircorresponding to a particular decision threshold (epitope (PEPI) count).The area under the ROC curve (AUC) is a measure of how well theclassifier can distinguish between two diagnostic groups (CTL responderor non-responder).

The analysis unexpectedly revealed that predicted epitope presentationby multiple class I HLAs of a subject (PEPI2+, PEPI3+, PEPI4+, PEPI5+,or PEPI6), was in every case a better predictor of CTL response thanepitope presentation by merely one or more HLA class I (PEPI1+,AUC=0.48, Table 12).

TABLE 12 Determination of diagnostic value of the PEPI biomarker by ROCanalysis Classifiers AUC PEPI1+ 0.48 PEPI2+ 0.51 PEPI3+ 0.65 PEPI4+ 0.52PEPI5+ 0.5  PEPI6+ 0.5 

The CTL response of an individual was best predicted by considering theepitopes of an antigen that could be presented by at least 3 HLA class Iof an individual (PEPI3+, AUC=0.65, Table 12). The threshold count ofPEPI3+(number of antigen-specific epitopes presented by 3 or more HLA ofan individual) that best predicted a positive CTL response was 1 (Table13). In other words, at least one antigen-derived epitope is presentedby at least 3 HLA class I of a subject (≥1 PEPI3+), then the antigen cantrigger at least one CTL clone, and the subject is a likely CTLresponder. Using the ≥1 PEPI3+ threshold to predict likely CTLresponders (“≥1 PEPI3+ Test”) provided 76% diagnostic sensitivity (Table13).

TABLE 13 Determination of the ≥ 1 PEPI3+ threshold to predict likely CTLresponders in the training dataset. PEPI3+ Count 1 2 3 4 5 6 7 8 9 10 1112 Sensitivity: 0.76 0.60 0.31 0.26 0.14 0.02 0 0 0 0 0 0 1-Specificity:0.59 0.24 0.21 0.15 0.09 0.06 0.06 0.03 0.03 0.03 0.03 0.03

Example 3—Validation of the ≥1 PEPI3+ Test

The test cohort of 81 datasets from 51 patients was used to validate the≥1 PEPI3+ threshold to predict an antigen-specific CTL response. Foreach dataset in the test cohort it was determined whether the ≥1 PEPI3+threshold was met (at least one antigen-derived epitope presented by atleast three class I HLA of the individual). This was compared with theexperimentally determined CTL responses reported from the clinicaltrials (Table 14).

The clinical validation demonstrated that a PEPI3+ peptide induce CTLresponse in an individual with 84% probability. 84% is the same valuethat was determined in the analytical validation of the PEPI3+prediction, epitopes that binds to at least 3 HLAs of an individual(Table 10). These data provide strong evidences that immune responsesare induced by PEPIs in individuals.

TABLE 14 Diagnostic performance characteristics of the ≥1 PEPI3+ Test (n= 81). Performance characteristic Description Result Positive 100% Thelikelihood that an individual that meets the ≥1 84% predictive [A/(A +B)] PEPI3+ threshold has antigen-specific CTL value (PPV) responsesafter treatment with immunotherapy. Sensitivity 100% The proportion ofsubjects with antigen-specific 75% [A/(A + C)] CTL responses aftertreatment with immunotherapy who meet the ≥1 PEPI3+ threshold.Specificity 100% The proportion of subjects without antigen-specific 55%[D/(B + D)] CTL responses after treatment with immunotherapy who do notmeet the ≥1 PEPI3+ threshold. Negative 100% The likelihood that anindividual who does not 42% predictive [D/(C + D)] meet the ≥1 PEPI3+threshold does not have value (NPV) antigen-specific CTL responses aftertreatment with immunotherapy. Overall 100% The percentage of predictionsbased on the ≥1 70% percent [(A + D)/N] PEPI3+ threshold that match theexperimentally agreement determined result, whether positive ornegative. (OPA) Fisher’s exact (p)   0.01

ROC analysis determined the diagnostic accuracy, using the PEPI3+ countas cut-off values (FIG. 2). The AUC value=0.73. For ROC analysis an AUCof 0.7 to 0.8 is generally considered as fair diagnostic.

A PEPI3+ count of at least 1 (≥1 PEPI3+) best predicted a CTL responsein the test dataset (Table 15). This result confirmed the thresholddetermined during the training (Table 12).

TABLE 15 Confirmation of the ≥ 1 PEPI3+ threshold to predict likely CTLresponders in the test/validation dataset. PEPI3+ Count 1 2 3 4 5 6 7 89 10 11 12 Sensitivity: 0.75 0.52 0.26 0.23 0.15 0.13 0.08 0.05 0 0 0 01-Specificity: 0.45 0.15 0.05 0 0 0 0 0 0 0 0 0

Example 4—the ≥1 PEPI3+ Test Predicts CD8+ CTL Reactivities

The ≥1 PEPI3+ Test was compared with a previously reported method forpredicting a specific human subject's CTL response to peptide antigens.

The HLA genotypes of 28 cervical cancer and VIN-3 patients that receivedthe HPV-16 synthetic long peptide vaccine (LPV) in two differentclinical trials were determined from DNA samples⁸ ⁹ ¹⁰. The LPV consistsof long peptides covering the HPV-16 viral oncoproteins E6 and E7. Theamino acid sequence of the LPV was obtained from these publications. Thepublications also report the T cell responses of each vaccinated patientto pools of overlapping peptides of the vaccine.

For each patient epitopes (9 mers) of the LPV that are presented by atleast three patient class I HLA (PEPI3+s) were identified and determinedtheir distribution among the peptide pools was determined. Peptides thatcomprised at least one PEPI3+(≥1 PEPI3+) were predicted to induce a CTLresponse. Peptides that comprised no PEPI3+ were predicted not to inducea CTL response.

The ≥1 PEPI3+ Test correctly predicted 489 out of 512 negative CTLresponses and 8 out of 40 positive CTL responses measured aftervaccination (FIG. 3A). Overall, the agreement between the ≥1 PEPI3+ Testand experimentally determined CD8+ T cell reactivity was 90% (p<0.001).

For each patient the distribution among the peptide pools of epitopesthat are presented by at least one patient class I HLA (≥1 PEPI1+, HLArestricted epitope prediction, prior art method) was also determined. ≥1PEPI1+ correctly predicted 116 out of 512 negative CTL responses and 37out of 40 positive CTL responses measured after vaccination (FIG. 3B).Overall, the agreement between the HLA restricted epitope prediction (≥1PEPI1+) and CD8+ T cell reactivity was 28% (not significant).

Example 5—Prediction of HLA Class II Restricted CD4+ Helper T CellEpitopes

The 28 cervical cancer and VIN-3 patients that received the HPV-16synthetic long peptide vaccine (LPV) in two different clinical trials(as detailed in Example 4) were investigated for CD4+T helper responsesfollowing LPV vaccination (FIG. 4A-B). The sensitivity of the predictionof HLA class II restricted epitopes was 78%, since the State of Art toolpredicted 84 positive responses (positive CD4+ T cell reactivity to apeptide pool for a person's DP alleles) out of 107 (sensitivity=78%).The specificity was 22% since it could rule out 7 negative responses outof 31. Overall, the agreement between HLA-restricted class II epitopeprediction and CD4+ T cell reactivity was 66%, which was statisticallynot significant.

Example 6—the ≥1 PEPI3+ Test Predicts T Cell Responses to Full LengthLPV Polypeptides

Using the same reported studies as Examples 4 and 5, the ≥1 PEPI3+ Testwas used to predict patient CD8+ and CD4+ T cell responses to the fulllength E6 and E7 polypeptide antigens of the LPV vaccine. Results werecompared to the experimentally determined responses were reported. TheTest correctly predicted the CD8+ T cell reactivity (PEPI3+) of 11 outof 15 VIN-3 patients with positive CD8+ T cell reactivity test results(sensitivity 73%, PPV 85%) and of 2 out of 5 cervical cancer patients(sensitivity 40%, PPV 100%). The CD4+ T cell reactivities (PEPI4+) werecorrectly predicted 100% both of VIN-3 and cervical cancer patients(FIGS. 5A-D).

Class I and class II HLA restricted PEPI3+ count was also observed tocorrelate with the reported clinical benefit to LPV vaccinated patients.Patients with higher PEPI3+ counts had either complete or partialresponse already after 3 months.

Example 7—Case Study

pGX3001 is an HPV16 based DNA vaccine containing full length E6 and E7antigens with a linker in between. pGX3002 is an HPV18 based DNA vaccinecontaining full length E6 and E7 antigens with a linker in between. APhase II clinical trial investigated the T cell responses of 17HPV-infected patients with cervical cancer who were vaccinated with bothpGX3001 and pGX3002 (VGX-3100 vaccination)′.

FIGS. 5A-D and FIG. 6 shows for two illustrative patients (patient 12-11and patient 14-5) the position of each epitope (9 mer) presented by atleast 1 (PEPI1+), at least 2 (PEPI2+), at least 3 (PEPI3+), at least 4(PEPI4+), at least 5 (PEPI5+), or all 6 (PEPI6) class I HLA of thesepatients within the full length sequence of the two HPV-16 and twoHPV-18 antigens.

Patient 12-11 had an overall PEPI1+ count of 54 for the combinedvaccines (54 epitopes presented by one or more class I HLA). Patient14-5 had a PEPI1+ count of 91. Therefore patient 14-5 has a higherPEPI1+ count than patient 12-11 with respect to the four HPV antigens.The PEPI1+s represent the distinct vaccine antigen specific HLArestricted epitope sets of patients 12-11 and 14-5. Only 27 PEPI1+s werecommon between these two patients.

For the PEPI3+ counts (number of epitopes presented by three or morepatient class I HLA), the results for patients 12-11 and 14-5 werereversed. Patient 12-11 had a PEPI3+ count of 8, including at least onePEPI3+ in each of the four HPV16/18 antigens. Patient 14-5 had a PEPI3+count of 0.

The reported immune responses of these two patients matched the PEPI3+counts, not the PEPI1+ counts. Patient 12-11 developed immune responsesto each of the four antigens post-vaccination as measured by ELISpot,whilst patient 14-5 did not develop immune responses to any of the fourantigens of the vaccines. A similar pattern was observed when the PEPI1+and PEPI3+ sets of all 17 patients in the trial were compared. There wasno correlation between the PEPI1+ count and the experimentallydetermined T cell responses reported from the clinical trial. However,we correlation between the T cell immunity predicted by the ≥1 PEPI3+Test and the reported T cell immunity was observed. The ≥1 PEPI3+ Testpredicted the immune responders to HPV DNA vaccine.

Moreover, the diversity of the patient's PEPI3+ set resembled thediversity of T cell responses generally found in cancer vaccine trials.Patients 12-3 and 12-6, similar to patient 14-5, did not have PEPI3+spredicting that the HPV vaccine could not trigger T cell immunity. Allother patients had at least one PEPI3 predicting the likelihood that theHPV vaccine can trigger T cell immunity. 11 patients had multiple PEPI3+predicting that the HPV vaccine likely triggers polyclonal T cellresponses. Patients 15-2 and 15-3 could mount high magnitude T cellimmunity to E6 of both HPV, but poor immunity to E7. Other patients 15-1and 12-11 had the same magnitude response to E7 of HPV18 and HPV16,respectively.

Example 8—Design of a Model Population for Conducting in Silico Trialsand Identifying Candidate Precision Vaccine Targets for Large Population

An in silico human trial cohort of 433 subjects with complete 4-digitHLA class I genotype (2×HLA-A*xx:xx; 2×HLA-B*xx:xx; 2×HLA-C*xx:xx) anddemographic information was compiled. This Model Population has subjectswith mixed ethnicity having a total of 152 different HLA alleles thatare representative for >85% of presently known allele G-groups.

A database of a “Big Population” containing 7,189 subjects characterizedwith 4-digit HLA genotype and demographic information was alsoestablished. The Big Population has 328 different HLA class I alleles.The HLA allele distribution of the Model Population significantlycorrelated with the Big Population (Table 16) (Pearson p<0.001).Therefore the 433 patient Model Population is representative for a 16times larger population.

The Model Population is representative for 85% of the human race asgiven by HLA diversity as well as HLA frequency.

TABLE 16 Statistical analysis of HLA distributions in “Model Population”vs. “Big Population”. Pearson Group name 1 Group name 2 R valueCorrelation P Value 433 Model 7,189 Big 0.89 Strong P < 0.001 PopulationPopulation

Example 9—in Silico Trials Based on the Identification of Multiple HLABinding Epitopes Predict the Reported T Cell Response Rates of ClinicalTrials

The objective of this study was to determine whether a model population,such as the one described in Example 8, may be used to predict CTLreactivity rates of vaccines, i.e. used in an in silico efficacy trials.

Twelve peptide vaccines derived from cancer antigens that induced T cellresponses in a subpopulation of subjects were identified from peerreviewed publications. These peptides have been investigated in clinicaltrials enrolling a total of 172 patients (4 ethnicities). T cellresponses induced by the vaccine peptides have been determined fromblood specimens and reported. The immune response rate as the percentageof study subjects with positive T cell responses measured in theclinical trials was determined (FIG. 7).

TABLE 17 Clinical trials conducted with peptide vaccines. Source PeptidePop. Peptide vaccines antigen length T cell assay (n) Ethnicity Ref.MMNLMQPKTQQTYTYD (SEQ ID NO: JUP 16mer Multimer 18 Canadian 12 103)staining GRGSTTTNYLLDRDDYRNTSD (SEQ ID ADA17 21mer Multimer 18 Canadian12 NO: 104) staining LKKGAADGGKLDGNAKLNRSLK (SEQ BAP31 22mer Multimer 18Canadian 12 ID NO: 105) staining FPPKDDHTLKFLYDDNQRPYPP (SEQ ID TOP2A22mer Multimer 18 Canadian 12 NO: 106) stainingRYRKPDYTLDDGHGLLRFKST (SEQ ID Abl-2 21mer Multimer 18 Canadian 12NO: 107) staining QRPPFSQLHRFLADALNT (SEQ ID NO: DDR1 18mer Multimer 18Canadian 12 108) staining ALDQCKTSCALMQQHYDQTSCFSSP ITGB8 25mer Multimer18 Canadian 12 (SEQ ID NO: 109) staining STAPPAHGVTSAPDTRPAPGSTAPP MUC-125mer Proliferation 80 Canadian 13 (SEQ ID NO: 110)YLEPGPVTA (SEQ ID NO: 111) gp100 9mer Tetramer 18 US 14MTPGTQSPFFLLLLLTVLTVV (SEQ ID MUC-1 21mer Cytotoxicity 10 Israeli 15NO: 112) SSKALQRPV (SEQ ID NO: 113) Bcr-Abl 9mer ELISPOT  4 US 16RMFPNAPYL (SEQ ID NO: 114) WT-1 9mer Multimer 24 US 17 stainingRMFPNAPYL (HLA-A*0201) (SEQ ID WT-1 9mer Cytokine 18 CEU 18 NO: 115)staining

The 12 peptides were investigated with the ≥1 PEPI3+ Test in each of the433 subjects of the Model Population described in Example 8. The “≥1PEPI3+ Score” for each peptide was calculated as the proportion ofsubjects in the Model Population having at least one vaccine derivedepitope that could bind to at least three subject-specific HLA class I(≥1 PEPI3+). If the corresponding clinical trial stratified patients forHLA allele selected population, the Model Population was also filteredfor subjects with the respective allele(s) (Example: WT1, HLA-A*0201).

The experimentally determined response rates reported from the trialswere compared with the ≥1 PEPI3+ Scores. The Overall Percentage ofAgreements (OPA) were calculated on the paired data (Table 18). A linearcorrelation between ≥1 PEPI3+ Score and response rate (R²=0.77) wasobserved (FIG. 7). This result shows that the identification of peptidespredicted to bind to multiple HLAs of an individual is useful to predictin silico the outcome of clinical trials.

TABLE 19 Comparison of ≥1 PEPI3+ Scores and CTL response rates of12 peptide vaccines. Response ≥1 PEPI3+ rate Score* Source (Clinical(Model Peptide vaccine antigen Trials) Population) OPAMMNLMQPKTQQTYTYD (SEQ ID JUP  0% 22% NA NO: 103)GRGSTTTNYLLDRDDYRNTSD (SEQ ADA17 11% 18% 61% ID NO: 104)LKKGAADGGKLDGNAKLNRSLK BAP31 11%  7% 64% (SEQ ID NO: 105)FPPKDDHTLKFLYDDNQRPYPP TOP2A 11% 39% 28% (SEQ ID NO: 106)RYRKPDYTLDDGHGLLRFKST (SEQ Abl-2 17% 12% 71% ID NO: 107)QRPPFSQLHRFLADALNT (SEQ ID DDR1 17%  5% 29% NO: 108)ALDQCKTSCALMQQHYDQTSCFSSP ITGB8 28% 31% 90% (SEQ ID NO: 109)STAPPAHGVTSAPDTRPAPGSTAPP MUC-1 20%  2% 10% (SEQ ID NO: 110)YLEPGPVTA (SEQ ID NO: 111) gp100 28%  4% 14% MTPGTQSPFFLLLLLTVLTVV (SEQMUC-1 90% 95% 95% ID NO: 112) SSKALQRPV (SEQ ID NO: 113) Bcr-  0%  0%100%  Abl RMFPNAPYL (SEQ ID NO: 114) WT-1 100%  78% 78%RMFPNAPYL (HLA-A*0201) (SEQ ID WT-1 81% 61% 75% NO: 115) *% subjects inthe Model Population with ≥1 vaccine derived PEPI3+

Example 10. In Silico Trials Based on the Identification of Multiple HLABinding Epitopes Predict the Reported T Cell Response Rates of ClinicalTrials II

Nineteen clinical trials with published immune response rates (IRR)conducted with peptide or DNA based vaccines were identified (Table 19).These trials involved 604 patients (9 ethnicities) and covered 38vaccines derived from tumor and viral antigens. Vaccine antigen specificCTL responses were measured in each study patient and the response ratein the clinical study populations was calculated and reported.

Each vaccine peptide of the 19 clinical trials was investigated with the≥1 PEPI3+ Test in each subject of the Model Population. The ≥1 PEPI3+Score for each peptide was calculated as the proportion of subjects inthe Model Population having at least one vaccine derived PEPI3+. Theexperimentally determined response rates reported from the trials werecompared with the PEPI Scores, as in Example 9 (Table 20). A linearcorrelation between the response rate and ≥1 PEPI3+ Score (R²=0.70) wasobserved (FIG. 8). This result confirms that the identification ofpeptides predicted to bind to multiple HLAs of an individual can predictT cell responses of subjects, and in silico trials can predict theoutcome of clinical trials.

TABLE 20 Response rates published in clinical trials. Pop. Race/Immunotherapy Type CTL assay (n) Ethnicity Ref. StimuVax peptideProliferation  80 Canadian 13 gp100 vaccine DNA Tetramer  18 US 14IMA901 phase I peptide ELISPOT  64 CEU 19 IMA901 phase II peptideMultimer  27 CEU staining ICT107 peptide ICC  15 US 20 ProstVac DNAELISPOT  32 CEU 87%, 21 Afr. Am. 12%, Hisp. 1% Synchrotope TA2M DNATetramer  26 US 22 MELITAC 12.1 peptide ELISPOT 167 US 23 WT1 vaccinepeptide Tetramer  22 Japanese 24 Ipilimumab (NY- Check- ICC  19 US  5ESO-1) point inhibitor ** VGX-3100 DNA ELISPOT  17 US  1 HIVIS-1 DNAELISPOT  12 CEU 98%, Asian 1%,  2 Hisp. 1% ImMucin peptide Cytotoxicity 10 Israeli 15 NY-ESO-1 OLP peptide IFN-gamma   7 Japanese  7 GVX301peptide Proliferation  14 CEU 25 WT1 vaccine peptide ELISPOT  12 US 26WT1 vaccine peptide ICC  18 CEU 18 DPX-0907* peptide Multimer  18Canadian 12 staining Melanoma peptide peptide ELISPOT  26 White 27vaccine

TABLE 21 Linear correlation between PEPI Score and response rate (R² =0.7). Clinical Trial ≥1 PEPI3+ Immunotherapy Response Rate Score* OPAStimuVax (failed to show 20% 2% 10% efficacy in Phase III) gp100 vaccine28%  4% 14% IMA901 phase I 74% 48% 65% IMA901 phase II 64% 48% 75%ICT107 33% 52% 63% ProstVac 45% 56% 80% Synchrotope TA2M 46% 24% 52%MELITAC 12.1 49% 47% 96% WT1 vaccine 59% 78% 76% Ipilimumab (NY-ESO-1*)72% 84% 86% VGX-3100 78% 87% 90% HIVIS-1 80% 93% 86% ImMucin 90% 95% 95%NY-ESO-1 OLP 100%  84% 84% GVX301 64% 65% 98% WT1 vaccine 83% 80% 96%WT1 vaccine 81% 61% 75% DPX-0907 61% 58% 95% Melanoma peptide vaccine52% 42% 81% *% subjects in the Model Population with ≥1 vaccine derivedPEPI3+

Example 11—in Silico Trial Based on the Identification of Multiple HLABinding Epitopes in a Multi-Peptide Vaccine Predict the ReportedClinical Trial Immune Response Rate

IMA901 is a therapeutic vaccine for renal cell cancer (RCC) comprising 9peptides derived from tumor-associated peptides (TUMAPs) that arenaturally presented in human cancer tissue. A total of 96 HLA-A*02+subjects with advanced RCC were treated with IMA901 in two independentclinical studies (phase I and phase II). Each of the 9 peptides ofIMA901 have been identified in the prior art as HLA-A2-restrictedepitopes. Based on currently accepted standards, they are all strongcandidate peptides to boost T cell responses against renal cancer in thetrial subjects, because their presence has been detected in renal cancerpatients, and because the trial patients were specifically selected tohave at least one HLA molecule capable of presenting each of thepeptides.

For each subject in the Model population how many of the nine peptidesof the IMA901 vaccine were capable of binding to three or more HLA wasdetermined. Since each peptide in the IMA901 vaccine is a 9 mer thiscorresponds to the PEPI3+ count. The results were compared with theimmune response rates reported for the Phase I and Phase II clinicaltrials (Table 22).

TABLE 22 Immune Response Rates in the Model Population and in twoclinical trials to IMA901 Model Population Immune responses to (HLA-A2+)Phase I Phase II TUMAPs (n = 180) (n = 27)* (n = 64)* No peptide 39% 25%36%  1 peptide 34% 44% 38% ≥2 peptides 27% 29% 26% (MultiPEPI Score) ≥3peptides  3% ND  3% *No of patients evaluated for immune responses

The phase I and phase II study results show the variability of theimmune responses to the same vaccine in different trial cohorts.Overall, however, there was a good agreement between response ratespredicted by the ≥2 PEPI3+ Test and the reported clinical responserates.

In a retrospective analysis, the clinical investigators of the trialsdiscussed above found that subjects who responded to multiple peptidesof the IMA901 vaccine were significantly (p=0.019) more likely toexperience disease control (stable disease, partial response) thansubjects who responded only to one peptide or had no response. 6 of 8subjects (75%) who responded to multiple peptides experienced clinicalbenefit in the trial, in contrast to 14% and 33% of 0 and 1 peptideresponders, respectively. The randomized phase II trial confirmed thatimmune responses to multiple TUMAPs were associated with a longeroverall survival.

Since the presence of PEPIs accurately predicted responders to TUMAPs,clinical responders to IMA901 are likely patients who can present ≥2PEPIs from TUMAPs. This subpopulation is only 27% of HLA-A*02 selectedpatients, and according to the clinical trial result, 75% of thissubpopulation is expected to experience clinical benefit. The sameclinical results suggest that 100% of patients would experience clinicalbenefit if patient selection is based on ≥3 PEPIs from TUMAPs, albeitthis population would represent only 3% of the HLA-A*02 selected patientpopulation. These results suggest that the disease control rate (stabledisease or partial response) is between 3% and 27% in the patientpopulation which was investigated in the IMA901 clinical trials. In theabsence of complete response, only a portion of these patients canexperience survival benefit.

These findings explain the absence of improved survival in the Phase IIIIMA901 clinical trial. These results also demonstrated that HLA-A*02enrichment of the study population was not sufficient to reach theprimary overall survival endpoint in the Phase III IMA901 trial. As theIMA901 trial investigators noted, there is a need for the development ofa companion diagnostic (CDx) to select likely responders to peptidevaccines. These findings also suggest that selection of patients with ≥2TUMAP specific PEPIs may provide sufficient enrichment to demonstratesignificant clinical benefit of IMA901.

Example 12—in Silico Trial Based on the Identification ofVaccine-Derived Multiple HLA Binding Epitopes Predict ReportedExperimental Clinical Response Rates

A correlation between the ≥2 PEPI3+ Score of immunotherapy vaccinesdetermined in the Model Population described in Example 8 and thereported Disease Control Rate (DCR, proportion of patients with completeresponses and partial responses and stable disease) determined inclinical trials was determined.

Seventeen clinical trials, conducted with peptide- and DNA-based cancerimmunotherapy vaccines that have published Disease Control Rates (DCRs)or objective response rate (ORR) were identified from peer reviewedscientific journals (Table 23). These trials involved 594 patients (5ethnicities) and covered 29 tumor and viral antigens. DCRs weredetermined according to the Response Evaluation Criteria in Solid Tumors(RECIST), which is the current standard for clinical trials, in whichclinical responses are based on changes in maximum cross-sectionaldimensions^(42, 43, 44). In case there was no available DCR data,objective response rate (ORR) data was used, which is also definedaccording to the RECIST guidelines.

Table 24 compares the ≥2 PEPI3+ Score for each vaccine in the ModelPopulation and the published DCR or ORR. A correlation between thepredicted and measured DCR was observed providing further evidence thatnot only the immunogenicity but also the potency of cancer vaccinesdepends on the multiple HLA sequences of individuals (R2=0.76) (FIG. 9).

TABLE 23 Clinical trials selected for Disease Control Rate (DCR)prediction. Assess- Study ment Immuno- Pop. pop./ HLA Adm. Dose Dosingtime therapy Antigen Sponsor Disease (n) Ethnicity restriction form (mg)schedule (weeks) Ref. IMA901 9 TAAs Immatics Renal cell 28 CEU A02 i.d.0.4 8× in 10 12 19 phase I cancer wks IMA901 9 TAAs Immatics Renal cell68 CEU A02 i.d 0.4 7× in 5 24 19 phase II cancer wks then 10× 3 wksIpilimumab NY- MSKCC Melanoma 19 US no i.v. 0.3 4× 24 5 ESO-1 3 every 310 wks HPV-SLP* HPV-16 Leiden VIN 20 CEU no s.c. 0.3 3× 12 9 E6, E7University every 3 wks HPV-SLP* Leiden HPV- 5 CEU no s.c. 0.3 3× 12 10University related every 3 (OR) cervical wks cancer gp100 -2 gp100 BMSMelanoma 136 US A*0201 s.c. 1 4× 12 28 peptides* every 3 wks ImmucinMuc-1 VaxilBio Myeloma 15 Israeli no s.c. 0.1 6×  12** 29 every 2 wksStimuVax Muc-1 Merck NSCLC 80 Canadian no s.c. 1 8× wkly 12 13, then 30every 6 wks VGX-3100 HPV- Inovio HPV- 125 US no i.m. 6 0, 4, 12 36 3116&18 related wks cervical cancer TSPP Thymidylate Siena CRC, 21 CEU nos.c. 0.1 3 × 3 12 32 peptide synthase University NSCLC, 0.2 wks vaccineGallbladder 0.3 carc., Breast-, Gastric cancer KIF20A-66 KIF20A ChibaMetastatic 29 Japanese A*2402 s.c. 1 2 cycles 12 33 peptide Tokushukaipancreatic 3 1, 8, 15, (OR) vaccine* Hospital cancer 22 days then every2 wks Peptide 3 TAAs Kumamoto HNSCC 37 Japanese A*2402 s.c. 1 8× wkly 1234 vaccine* University then every 4 wks 7-peptide 7 TAAs KinkiMetastatic 30 Japanese A*2402 s.c. 1 Cycles: 10 35 cocktail Universitycolorectal 5× wkly (OR) vaccine* cancer then 1 wk rest GVX301* hTERTUniversity Prostate 14 Japanese A02 i.d. 0.5 1, 3, 5, 12 25 Genoa and 7,14, renal 21, 35, cancer 63 days MAGE-A3 MAGE- Abramson Multiple 26 USno s.c. 0.3 14, 42, 24 36 Trojan* A3 Cancer myeloma 90, 120, Center 150days PepCan HPV-16 University CIN2/3 23 US no i.m. 0.05 4 × 3 24 37 E6of 0.1 wks Arkansas 0.25 0.5 Melanoma Tyrosinase, University Melanoma 26US A1, A2 or s.c. 0.1 6 cycles:  6 27 peptide gp100 of A3 0, 7, 14,vaccine* Virginia 28, 35, 42 days *Montanide ISA51 VG as adjuvant**Disease response was assessed according to the International MyelomaWorking Group response criteria45

TABLE 24 The Disease Control Rates (DCRs) and MultiPEPI Scores(predicted DCR) in 17 clinical trials. MultiPEPI Score OverallPercentage Immunotherapy DCR (Predicted DCR) of Agreement IMA901 phase I43% 27% 61% IMA901 phase II 22% 27% 81% Ipilimumab 60% 65% 92% HPV-SLP60% 70% 86% HPV-SLP 62% 70% 89% gp100-2 peptides 15% 11% 73% Immucin 73%59% 81% StimuVax  0%  0% 100%  VGX-3100 50% 56% 89% TSPP peptide vaccine48% 31% 65% KIF20A-66 peptide 26%  7% 27% vaccine Peptide vaccine 27%10% 37% 7-peptide cocktail 10%  9% 90% vaccine GVX301 29%  7% 24%MAGE-A3 Trojan 35% 10% 29% PepCan 52% 26% 50% Melanoma peptide 12%  6%50% vaccine

Example 13 in Silico Trials Based on the Identification of Multiple HLABinding Epitopes Predict the Reported Cellular Immune Response Rates toa Vaccine Targeting a Mutational Antigen

The epidermal growth factor receptor variant III (EGFRvIII) is atumor-specific mutation broadly expressed in glioblastoma multiforme(GBM) and other neoplasms. The mutation comprises an in-frame deletionof 801 bp from the extracellular domain of the EGFR that splits a codonand yields a novel glycine at the fusion junction.^(1, 2) This mutationencodes a constitutively active tyrosine kinase that increases tumorformation and tumor cell migration and enhances resistance againstradiation and chemotherapy.^(3, 4, 5, 6, 7, 8, 9) This insertion resultsin a tumor-specific epitope which is not found in normal adult tissuesmaking EGFRvIII a suitable target candidate for antitumorimmunotherapy.¹⁰ Rindopepimut is a 13-amino-acid peptide vaccine(LEEKKGNYVVTDHC (SEQ ID NO: 189)) spanning the EGFRvIII mutation with anadditional C-terminal cysteine residue.¹¹

In a phase II clinical study, the peptide conjugated to keyhole limpethemocyanin (KLH) was administered to newly diagnosed EGFRvIII-expressingGBM patients. The first three vaccinations were given biweekly, starting4 weeks after the completion of radiation. Subsequent vaccines weregiven monthly until radiographic evidence of tumor progression or death.All vaccines were given intradermally in the inguinal region.Immunologic evaluation showed only 3 out of 18 patients developingcellular immune response assessed by DTH reaction test.

An in silico trial with the Model Population of 433 subjects withRindopepimut sequence was conducted. 4 out of 433 subjects had PEPI3+,confirming the low immunogenicity found in the phase II study (Table25).

TABLE 25 Results of clinical trial and in silico study RespondersResponse rate Clinical trial (Phase II) 3/18  16.6% In silico study(PEPI3+ Test) 4/433    1%

An HLA map of the Rindopepimut on the HLA alleles of the subjects in theModel Population (FIG. 10) illustrates that very few HLA-A and HLA-Calleles can bind the vaccine epitopes which explains the lack of PEPI3+in the in silico cohort.

In a recent phase III clinical study the ineffectiveness was furtherdemonstrated when 745 patients were enrolled and randomly assigned toRindopepimut and temozolomide (n=371) or control and temozolomide(n=374) arms.¹² The trial was terminated for ineffectiveness after theinterim analysis. The analysis showed no significant difference inoverall survival: median overall survival was 20.1 months (95% CI18.5-22.1) in the Rindopepimut group versus 20.0 months (18.1-21.9) inthe control group (HR 1.01, 95% CI 0.79-1.30; p=0.93).

REFERENCES FOR EXAMPLE 13

-   1 Bigner et al. Characterization of the epidermal growth factor    receptor in human glioma cell lines and xenografts. Cancer Res 1990;    50: 8017-22.-   2 Libermann et al. Amplification, enhanced expression and possible    rearrangement of EGF receptor gene in primary human brain tumours of    glial origin. Nature 1985; 313: 144-7.-   3 Chu et al. Receptor dimerization is not a factor in the signalling    activity of a transforming variant epidermal growth factor receptor    (EGFRvIII). Biochem J 1997; 324: 855-61.-   4 Batra et al. Epidermal growth factor ligand-independent,    unregulated, cell-transforming potential of a naturally occurring    human mutant EGFRvIII gene. Cell Growth Differ 1995; 6: 1251-9.-   5 Nishikawa et al. A mutant epidermal growth factor receptor common    in human glioma confers enhanced tumorigenicity. PNAS 1994; 91:    7727-31.-   6 Lammering et al. Inhibition of the type III epidermal growth    factor receptor variant mutant receptor by dominant-negative    EGFR-CD533 enhances malignant glioma cell radiosensitivity. Clin    Cancer Res 2004; 10: 6732-43.-   7 Nagane et al. A common mutant epidermal growth factor receptor    confers enhanced tumorigenicity on human glioblastoma cells by    increasing proliferation and reducing apoptosis. Cancer Res 1996;    56: 5079-86.-   8 Lammering et al. Radiation-induced activation of a common variant    of EGFR confers enhanced radioresistance. Radiother Oncol 2004; 72:    267-73.-   9 Montgomery et al. Expression of oncogenic epidermal growth factor    receptor family kinases induces paclitaxel resistance and alters    β-tubulin isotype expression. J Biol Chem 2000; 275: 17358-63.-   10 Humphrey et al. Anti-synthetic peptide antibody reacting at the    fusion junction of deletion-mutant epidermal growth factor receptors    in human glioblastoma. PNAS 1990; 87: 4207-11.-   11 Sampson et al. Immunologic Escape After Prolonged    Progression-Free Survival With Epidermal Growth Factor Receptor    Variant III Peptide Vaccination in Patients With Newly Diagnosed    Glioblastoma. J Clin Oncol 28:4722-4729.-   12 Weller at al. Rindopepimut with temozolomide for patients with    newly diagnosed, EGFRvIII-expressing glioblastoma (ACT IV): a    randomised, double-blind, international phase 3 trial. Lancet Oncol    2017; 18(10): 1373-1385.

Example 14. Multiple HLA Binding Peptides of Individuals can PredictImmune-Toxicity

Thrombopoietin (TPO) is a highly immunogenic protein drug causingtoxicity in many patients. EpiVax/Genentech used State of Art technologyto identify class II HLA restricted epitopes and found that the mostimmunogenic region of the TPO is located in the C-terminal end of TPO(US20040209324 A1).

According to the present disclosure we defined the multiple class II HLAbinding epitopes (PEPI3+s) from TPO in 400 HLA class II genotyped USsubjects were determined. Most of the PEPI3+ peptides of theseindividuals located within the N terminal region of the TPO between1-165 amino acids. PEPI3+ were sporadically identified in some subjectsalso in the C terminal region. However, our results were different fromthe State of Art.

The published literature confirmed the disclosed results, demonstratingexperimental proof for the immunotoxic region being located at theN-terminal end of TPO^(40, 41). Most individuals treated with TPO drugmade anti-drug antibodies (ADA) ADA against this region of the drug.These antibodies not only abolished the therapeutic effect of the drugbut also caused systemic adverse events, i.e. immune-toxicity, likeantibody-dependent cytotoxicity (ADCC) and complement-dependentcytotoxicity associated with thrombocytopenia, neutropenia and anemia.These data demonstrate that the identification of multiple HLA bindingpeptides of individuals predicts the immune-toxicity of TPO. Therefore,the disclosure is useful to identify the toxic immunogenic region ofdrugs, to identify subjects who likely experience immune-toxicity fromdrugs, to identify regions of a polypeptide drug that may be targeted byADAs, and to identify subjects who likely experience ADA.

Example 15 Personalised Immunotherapy Composition for Treatment ofOvarian Cancer

This example describes the treatment of an ovarian cancer patient with apersonalised immunotherapy composition, wherein the composition wasspecifically designed for the patient based on her HLA genotype based onthe disclosure described herein. This Example and Example 16 belowprovide clinical data to support the principals regarding binding ofepitopes by multiple HLA of a subject to induce a cytotoxic T cellresponse on which the present disclosure is based.

The HLA class I and class II genotype of metastatic ovarianadenocarcinoma cancer patient XYZ was determined from a saliva sample.

To make a personalized pharmaceutical composition for patient XYZthirteen peptides were selected, each of which met the following twocriteria: (i) derived from an antigen that is expressed in ovariancancers, as reported in peer reviewed scientific publications; and (ii)comprises a fragment that is a T cell epitope capable of binding to atleast three HLA class I of patient XYZ (Table 26). In addition, eachpeptide is optimized to bind the maximum number of HLA class II of thepatient.

TABLE 26 XYZ ovarian cancer patient's personalized vaccine MAX MAX XYZ'sTarget Antigen HLA HLA vaccine Antigen Expression 20mer peptidesclass I  class II P0001_P1 AKAP4 89% NSLQKQLQAVLQWIAASQFN 3 5(SEQ ID NO: 116) P0001_P2 BORIS 82% SGDERSDEIVLTVSNSNVEE 4 2(SEQ ID NO: 117) P0001_P3 SPAG9 76% VQKEDGRVQAFGWSLPQKYK 3 3(SEQ ID NO: 118) P0001_P4 OY-TES-1 75% EVESTPMIMENIQELIRSAQ 3 4(SEQ ID NO: 119) P0001_P5 SP17 69% AYFESLLEKREKTNFDPAEW 3 1(SEQ ID NO: 120) P0001_P6 WT1 63% PSQASSGQARMFPNAPYLPS 4 1(SEQ ID NO: 121) P0001_P7 HIWI 63% RRSIAGEVASINEGMTRWFS 3 4(SEQ ID NO: 122) P0001_P8 PRAME 60% MQDIKMILKMVQLDSIEDLE 3 4(SEQ ID NO: 123) P0001_P9 AKAP-3 58% ANSVVSDMMVSIMKTLKIQV 3 4(SEQ ID NO: 124) P0001_P10 MAGE-A4 37% REALSNKVDELAHFLLRKYR 3 2(SEQ ID NO: 125) P0001_P11 MAGE-A9 37% ETSYEKVINYLVMLNAREPI 3 4(SEQ ID NO: 126) P0001_P12a MAGE-A10 52% DVKEVDPTGHSFVLVTSLGL 3 4(SEQ ID NO: 127) P0001_P12b BAGE 30% SAQLLQARLMKEESPVVSWR 3 2(SEQ ID NO: 128)

Eleven PEPI3 peptides in this immunotherapy composition can induce Tcell responses in XYZ with 84% probability and the two PEPI4 peptides(POC01-P2 and POC01-P5) with 98% probability, according to thevalidation of the PEPI Test shown in Table 10. T cell responses target13 antigens expressed in ovarian cancers. Expression of these cancerantigens in patient XYZ was not tested. Instead the probability ofsuccessful killing of cancer cells was determined based on theprobability of antigen expression in the patient's cancer cells and thepositive predictive value of the ≥1 PEPI3+ Test (AGP count). AGP countpredicts the effectiveness of a vaccine in a subject: Number of vaccineantigens expressed in the patient's tumor (ovarian adenocarcinoma) withPEPI. The AGP count indicates the number of tumor antigens that vaccinerecognizes and induces a T cell response against the patient's tumor(hit the target). The AGP count depends on the vaccine-antigenexpression rate in the subject's tumor and the HLA genotype of thesubject. The correct value must be between 0 (no PEPI presented byexpressed antigen) and maximum number of antigens (all antigens areexpressed and present a PEPI).

The probability that patient XYZ will express one or more of the 12antigens is shown in FIGS. 11A-B. AGP95=5, AGP50=7.9, mAGP=100%, AP=13.

A pharmaceutical composition for patient XYZ may be comprised of atleast 2 from the 13 peptides (Table 26), because the presence in avaccine or immunotherapy composition of at least two polypeptidefragments (epitopes) that can bind to at least three HLA of anindividual (≥2 PEPI3+) was determined to be predictive for a clinicalresponse. The peptides are synthetized, solved in a pharmaceuticallyacceptable solvent and mixed with an adjuvant prior to injection. It isdesirable for the patient to receive personalized immunotherapy with atleast two peptide vaccines, but preferable more to increase theprobability of killing cancer cells and decrease the chance of relapse.

For treatment of patient XYZ the 12 peptides were formulated as 4×¾peptide (POC01/1, POC01/2, POC01/3, POC01/4). One treatment cycle isdefined as administration of all 13 peptides within 30 days.

Patient history:Diagnosis: Metastatic ovarian adenocarcinoma

Age: 51

Family anamnesis: colon and ovary cancer (mother) breast cancer(grandmother)Tumor pathology:

BRCA1-185delAG, BRAF-D594Y, MAP2K1-P293S, NOTCH1-S2450N

-   -   2011: first diagnosis of ovarian adenocarcinoma; Wertheim        operation and chemotherapy; lymph node removal    -   2015: metastasis in pericardial adipose tissue, excised    -   2016: hepatic metastases    -   2017: retroperitoneal and mesenteric lymph nodes have        progressed; incipient peritoneal carcinosis with small        accompanying ascites

Prior Therapy:

-   -   2012: Paclitaxel-carboplatin (6×)    -   2014: Caelyx-carboplatin (lx)    -   2016-2017 (9 months): Lymparza (Olaparib) 2×400 mg/day, oral    -   2017: Hycamtin inf. 5×2.5 mg (3× one seria/month)

PIT vaccine treatment began on 21 Apr. 2017.

TABLE 27 Patient XYZ peptide treatment schedule Vaccinations Lot #1^(st) cycle 2^(nd) cycle 3^(rd) cycle 4^(th) cycle POC01/1 N172721.04.2017 16.06.2017 30.08.2017 19.10.2017 POC01/2 N1728 28.04.201731.05.2017 POC01/3 N1732 16.06.2017 02.08.2017 20.09.2017 POC01/4 N173615.05.2017 06.07.2017Patient' tumor MRI findings (Baseline Apr. 15, 2016)

-   -   Disease was confined primarily to liver and lymph nodes. The use        of MRI limits detection of lung (pulmonary) metastasis    -   May 2016-January 2017: Olaparib treatment    -   Dec. 25, 2016 (before PIT vaccine treatment) There was dramatic        reduction in tumor burden with confirmation of response obtained        at FU2    -   January-March 2017—TOPO protocol (topoisomerase)    -   Apr. 6, 2017 FU3 demonstrated regrowth of existing lesions and        appearance of new lesions leading to disease progression    -   Apr. 21, 2017 START PIT    -   Jul. 21, 2017 (after the 2^(nd) Cycle of PIT) FU4 demonstrated        continued growth in lesions and general enlargement of pancreas        and abnormal para pancreatic signal along with increased ascites    -   Jul. 26, 2017—CBP+Gem+Avastin    -   Sep. 20, 2017 (after 3 Cycles of PIT) FU5 demonstrated reversal        of lesion growth and improved pancreatic/parapancreatic signal.        The findings suggest pseudo progression    -   Nov. 28, 2017 (after 4 Cycles of PIT) FU6 demonstrated best        response with resolution of non target lesions        MRI data for patient XYZ is shown in Table 28 and FIG. 12.

TABLE 28 Summary Table of Lesions Responses Baseline FU1 FU2 FU3 FU4 FU5FU6 Lesion/ (% Δ (% Δ (% Δ (% Δ (% Δ (% Δ (% Δ Best PD Time from fromfrom from from from from Response Time Point BL) BL) BL) BL) BL) BL) BL)Cycle Point TL1 NA −56.1 −44.4 −44.8 +109.3 −47.8 −67.3 FU6 FU4 TL2 NA−100.0 −100.0 −47.1 −13.1 −100.0 −100.0 FU1 FU3 TL3 NA −59.4 −62.3 −62.0−30.9 −66.7 −75.9 FU6 FU4 TL4 NA −65.8 −100.0 −100.0 −100.0 −100.0−100.0 FU2 NA SUM NA −66.3 −76.0 −68.9 −23.5 −78.2 −85.2 FU6 FU4

Example 16 Design of Personalised Immunotherapy Composition forTreatment of Breast Cancer

The HLA class I and class II genotype of metastatic breast cancerpatient ABC was determined from a saliva sample. To make a personalizedpharmaceutical composition for patient ABC twelve peptides wereselected, each of which met the following two criteria: (i) derived froman antigen that is expressed in breast cancers, as reported in peerreviewed scientific publications; and (ii) comprises a fragment that isa T cell epitope capable of binding to at least three HLA class I ofpatient ABC (Table 29). In addition, each peptide is optimized to bindthe maximum number of HLA class II of the patient. The twelve peptidestarget twelve breast cancer antigens. The probability that patient ABCwill express one or more of the 12 antigens is shown in FIG. 13.

TABLE 29 12 peptides for ABC breast cancer patient BRCO9 vaccine TargetAntigen MAXHLA MAXHLA peptides Antigen Expression 20mer peptide Class IClass II PBRC01_cP1 FSIP1 49% ISDTKDYFMSKTLGIGRLKR 3 6 (SEQ ID NO: 129)PBRC01_cP2 SPAG9 88% FDRNTESLFEELSSAGSGLI 3 2 (SEQ ID NO: 130)PBRC01_cP3 AKAP4 85% SQKMDMSNIVLMLIQKLLNE 3 6 (SEQ ID NO: 131)PBRC01_cP4 BORIS 71% SAVFHERYALIQHQKTHKNE 3 6 (SEQ ID NO: 132)PBRC01_cP5 MAGE-A11 59% DVKEVDPTSHSYVLVTSLNL 3 4 (SEQ ID NO: 133)PBRC01_cP6 NY-SAR-35 49% ENAHGQSLEEDSALEALLNF 3 2 (SEQ ID NO: 134)PBRC01_cP7 HOM-TES-85 47% MASFRKLTLSEKVPPNHPSR 3 5 (SEQ ID NO: 135)PBRC01_cP8 NY-BR-1 47% KRASQYSGQLKVLIAENTML 3 6 (SEQ ID NO: 136)PBRC01_cP9 MAGE-A9 44% VDPAQLEFMFQEALKLKVAE 3 8 (SEQ ID NO: 137)PBRC01_cP10 SCP-1 38% EYEREETRQVYMDLNNNIEK 3 3 (SEQ ID NO: 138)PBRC01_cP11 MAGE-A1 37% PEIFGKASESLQLVEGIDVK 3 3 (SEQ ID NO: 139)PBRC01_cP12 MAGE-C2 21% DSESSFTYTLDEKVAELVEF 4 2 (SEQ ID NO: 140)Predicted efficacy: AGP95=4; 95% likelihood that the PIT Vaccine inducesCTL responses against 4 CTAs expressed in the breast cancer cells ofBRC09. Additional efficacy parameters: AGP50=6.3, mAGP=100%, AP=12.Detected efficacy after the 1^(st) vaccination with all 12 peptides: 83%reduction of tumor metabolic activity (PET CT data).

For treatment of patient ABC the 12 peptides were formulated as 4×3peptide (PBR01/1, PBR01/2, PBR01/3, PBR01/4). One treatment cycle isdefined as administration of all 12 different peptide vaccines within 30days.

Patient historyDiagnosis: bilateral metastatic breast carcinoma: Right breast is ERpositive, PR negative, Her2 negative; Left Breast is ER, PR and Her2negative.First. diagnosis: 2013 (4 years before PIT vaccine treatment)2016: extensive metastatic disease with nodal involvement both above andbelow the diaphragm. Multiple liver and pulmonary metastases.2016-2017 treatment: Etrozole, Ibrance (Palbociclib) and Zoladex

Results

Mar. 7, 2017: Prior PIT Vaccine treatmentHepatic multi-metastatic disease with truly extrinsic compression of theorigin of the choledochal duct and massive dilatation of the entireintrahepatic biliary tract. Celiac, hepatic hilar and retroperitonealadenopathyMay 26, 2017: After 1 cycle of PITDetected efficacy: 83% reduction of tumor metabolic activity (PET CT)liver, lung lymphnodes and other metastases. Detected safety: SkinreactionsLocal inflammation at the site of the injections within 48 hoursfollowing vaccine administrations

Follow up:

BRC-09 was treated with 5 cycles of PIT vaccine. She was feeling verywell and she refused a PET CT examination in September 2017. In Novembershe had symptoms, PET CT scan showed progressive disease, but sherefused all treatments. In addition, her oncologist found out that shedid not take Palbocyclib since spring/summer. Patient ABC passed away inJanuary 2018.

The combination of pablocyclib and the personalised vaccine was likelyto have been responsible for the remarkable early response observedfollowing administration of the vaccine. Palbocyclib has been shown toimprove the activity of immunotherapies by increases CTA presentation byHLAs and decreasing the proliferation of Tregs: (Goel et al. Nature.2017:471-475). The PIT vaccine may be used as add-on to the state-of-arttherapy to obtain maximal efficacy.

Example 17. Breast Cancer Vaccine Design for Large Population andComposition

We used the PEPI3+ Test described above to design peptides for use inbreast cancer vaccines that are effective in a large percentage ofpatients, taking into account the heterogeneities of both tumourantigens and patients' HLAs.

Breast cancer CTAs were identified and ranked based on the overallexpression frequencies of antigens found in breast cancer tumor samplesas reported in peer reviewed publications (Chen et al. MultipleCancer/Testis Antigens Are Preferentially Expressed in Hormone-ReceptorNegative and High-Grade Breast Cancers. Plos One 2011; 6(3): e17876;Kanojia et al. Sperm-Associated Antigen 9, a Novel Biomarker for EarlyDetection of Breast Cancer. Cancer Epidemiol Biomarkers Prev 2009;18(2):630-639.; Saini et al. A Novel Cancer Testis Antigen, A-KinaseAnchor Protein 4 (AKAP4) Is a Potential Biomarker for Breast Cancer.Plos One 2013; 8(2): e57095).

For select CTAs we used the PEPI3+ Test and the Model Populationdescribed in Example 8 to identify the 9 mer epitopes (PEPI3+s) that aremost frequently presented by at least 3HLAs of the individuals in theModel Population. We refer to these epitopes herein as “bestEPIs”. Anillustrative example of the “PEPI3+ hotspot” analysis and bestEPIidentification is shown in FIG. 14 for the PRAME antigen.

We multiplied the reported expression frequency for each CTA (N %) bythe frequency of the PEPI3+ hotspots in the Model Population (B %) toidentify the T cell epitopes (9 mers) that will induce an immuneresponse against breast cancer antigens in the highest proportion ofindividuals (Table 30). We then selected 15 mers encompassing each ofthe selected 9 mers (Table 30). The 15 mers were selected to bind tomost HLA class II alleles of most subjects, using the process describedin Example 22 below. These 15 mers can induce both CTL and T helperresponses in the highest proportion of subjects.

TABLE 30 BestEPI list for selecting breast cancer peptidevaccine composition. Ntotal: number of samplesanalyzed for the expression of the certainantigen; N+: number of individuals expressingthe certain antigen; N %: expression frequencyof the certain antigen; B %: bestEPI frequency,ie. the percentage of individuals having thebestEPI within the model population; N % * B %:expression frequency multiplied by the bestEPI frequency.Antigen Information BestEPIs Gene length Ntotal N+ N % SEQ Position B%N % * B % AKAP-4 854 91 77 85% YLMNRPQNL 167 52% 44% (SEQ ID NO: 1)AKAP-4 854 91 77 85% MMAYSDTTM 1 49% 41% (SEQ ID NO: 2) BORIS 663 58 4171% FTSSRMSSF 264 57% 40% (SEQ ID NO: 3) AKAP-4 854 91 77 85% YALGFQHAL121 46% 39% (SEQ ID NO: 4) SPAG9 1321 100 88 88% SLLPTM 964 43% 38%(SEQ ID NO: 5) SPAG9 1321 100 88 88% FTVCNSHVL 785 36% 31% (SEQ IDNO: 6) BORIS 663 58 41 71% MAFVTSGEL 320 44% 31% (SEQ ID NO: 7) PRAME509 100 55 55% YLHARLREL 462 52% 28% (SEQ ID NO: 8) SPAG9 1321 100 8888% VMSERVSGL 19 28% 25% (SEQ ID NO: 9) BORIS 663 58 41 71% FTQSGTMKI407 35% 25% (SEQ ID NO: 10) NY-SAR-35 255 29 14 48% FSSSGTTSF 163 45%22% (SEQ ID NO: 11) MAGE-A9 315 142 63 44% FMFQEALKL 102 49% 22% (SEQ IDNO: 12) NY-SAR-35 255 29 14 48% FVLANGHIL 97 42% 21% (SEQ ID NO: 13)PRAME 509 100 55 55% KAMVQAWPF 70 37% 20% (SEQ ID NO: 14) NY-BR-1 1341131 61 47% YSCDSRSLF 424 39% 18% (SEQ ID NO: 15) Survivin 142 167 11871% RAIEQLAAM 133 26% 18% (SEQ ID NO: 16) MAGE-A11 429 135 79 59%AMDAIFGSL 184 23% 14% (SEQ ID NO: 17) HOM-TES-85 313 100 47 47%MASERKLTL 1 29% 13% (SEQ ID NO: 18) MAGE-A9 315 142 63 44% SSISVYYTL 6730% 13% (SEQ ID NO: 19) NY-BR-1 1341 131 61 47% SAFEPATEM 584 27% 12%(SEQ ID NO: 20)

Then we designed 31, 30 mer peptides. Each consists of two optimized 15mer fragments, generally from different frequent CTAs, arranged end toend, each fragment comprising one of the 9 mers (BestEPIs) from Table30. Nine of these 30 mer peptides were selected for a panel of peptides,referred to as PolyPEPI915 (Table 31). Expression frequencies for the 10CTAs targeted by PolyPEPI915, singly and in combination, are shown inFIG. 15.

TABLE 31 Selected Breast Cancer Vaccine peptides for PolyPEPI915panel/composition HLAI* HLAII** TREOSID Source Antigen Peptide (30mer)(CD8) (CD4) BCV900-4-1 SPAG9/AKAP4 GNILDSFTVCNSHVLLQKYALGFQHALSPS 53%75% (SEQ ID NO: 59) BCV900-4-2 BORIS/NY-SAR-35NMAFVTSGELVRHRRESSSGTTSFKCFAPF 65% 46% (SEQ ID NO: 60) BCV900-3-3NY-BR-1/SURVIVIN YSCDSRSLFESSAKITAKKVRRAIEQLAAM 55% 11% (SEQ ID NO: 52)BCV900-3-4 AKAP-4/BORIS MMAYSDTTMMSDDIDHTRFTQSGTMKIHIL 72% 45%(SEQ ID NO: 53) BCV900-4-5 SPAG9/BORIS AQKPISSLLPTMWLGAMFTSSRMSSENRHMK72% 50% (SEQ ID NO: 61) BCV900-5-6 HomTes85/MageA11MASFRKLTLSEKVPPSPTAMDAIFGSLSDE 45% 16% (SEQ ID NO: 63) BCV900-5-7AKAP4/PRAME DQVNIDYLMNRPQNLRHSQTLKAMVQAWPF 64% 33% (SEQ ID NO: 64)BCV900-5-8 NYSAR/SPAG9 CSGSSYFVLANGHILSGAVMSERVSGLAGS 46% 48%(SEQ ID NO: 65) BCV900-3-9 PRAME/MAGE-A9 LERLAYLHARLRELLQLEFMFQEALKLKVA73% 100% (SEQ ID NO: 58) PolyPEPI915 (9 peptide together) 96% 100%*Percentage of individuals having CD8+ T cell specific PEPI3+ within theModel Population (n = 433). **Percentage of individuals having CD4+ Tcell specific PEPI4+ within the Model Population (n = 433).

Characterization of PolyPEPI915

Tumor heterogeneity can be addressed by including peptide sequences thattarget multiple CTAs in a vaccine or immunotherapy regime. ThePolyPEPI915 composition targets 10 different CTAs. Based on the antigenexpression rates for these 10 CTAs, we modelled the predicted averagenumber of expressed antigens (AG50) and the minimum number of expressedantigens with 95% likelihood (AG95) in the cancer cells. 95% ofindividuals expressed minimum 4 of the 10 target antigens (AG95=4) asshown by the antigen expression curve in FIGS. 16A-B.

The AG values described above characterize a vaccine independently fromthe target patient population. They can be used to predict thelikelihood that a specific cancer (e.g. breast cancer) expressesantigens targeted by a specific vaccine or immunotherapy composition. AGvalues are based on known tumor heterogeneity, but do not take HLAheterogeneity into account.

HLA heterogeneity of a certain population can be characterised from theviewpoint of an immunotherapy or vaccine composition by the number ofantigens representing PEPI3+. These are the vaccine-specific CTAantigens for which ≥1 PEPI3+ is predicted, referred to herein as the“AP”. The average number of antigens with PEPI3+(AP50) shows how thevaccine can induce immune response against the antigens targeted by thecomposition (breast cancer vaccine specific immune response). ThePolyPEPI915 composition can induce immune response against an average of5.3 vaccine antigens (AP50=5.30) and 95% of the Model Population caninduce immune response against at least one vaccine antigen(AP95=1)(FIGS. 17A-B).

Vaccines can be further characterized by AGP values that refers toantigens with PEPIs”. This parameter is the combination of the previoustwo parameters: (1) AG is depending on the antigen expressionfrequencies in the specific tumor type but not on the HLA genotype ofindividuals in the population, and (2) AP is depending on the HLAgenotype of individuals in a population without taking account theexpression frequencies of the antigen. The AGP is depending on both, theexpression frequencies of vaccine antigens in the disease and the HLAgenotype of individuals in a population.

Combining the data of AG of breast cancer and AP in the Model Populationwe determined the AGP value of PolyPEPI915 that represents theprobability distribution of vaccine antigens that are induce immuneresponses against antigens expressed in breast tumors. For PolyPEPI915,the AGP50 value in the Model Population is 3.37. The AGP92=1, means that92% of the subjects in the Model Population induce immune responsesagainst at least one expressed vaccine antigen (FIGS. 18A-B).

Example 18—Likely Responder Patient Selection Using Companion DiagnosticTests for Vaccines

The likelihood that a specific patient will have an immune response or aclinical response to treatment with one or more cancer vaccine peptides,for example as described above, can be determined based on (i) theidentification of PEPI3+ within the vaccine peptide(s) (9 mer epitopescapable of binding at least three HLA of the patient); and/or (ii) adetermination of target antigen expression in cancer cells of thepatient, for example as measured in a tumour biopsy. In some cases bothparameters are ideally determined and the optimal combination of vaccinepeptides is selected for use in treatment of the patient. However,PEPI3+ analysis alone may be used if a determination of the expressedtumour antigens, for example by biopsy, is not possible, not advised, orunreliable due to biopsy error (i.e. biopsy tissue samples taken from asmall portion of the tumor or metastasised tumors do not represent thecomplete repertoire of CTAs expressed in the patient).

Example 19—Comparison of PolyPEPI915 with Competing Breast CancerVaccines

We used the in silico clinical trial model described in above to predictthe immune response rates of competing breast cancer vaccines that havebeen investigated in clinical trials (Table 32). The immune responserate of these products were between 3% and 91%.

The single peptide vaccines were immunogenic in 3%-23% of individuals.In comparison, the 30 mer peptides described in Example 18 above (Table29) were each immunogenic in from 44% to 73% of individuals in the samecohorts. This result represents substantial improvement inimmunogenicity of each peptide in PolyPEPI915.

Competing combination peptide products immune response rates werebetween 10-62%. The invented PolyPEPI915 combination product were 96% inthe Model Population and 93% in a breast cancer patient population,representing improvement in immunogenicity.

TABLE 32 Predicted immune response rates of competing breast cancervaccines Predicted immune response rates* 433 normal 90 patients Targetdonors (Model with breast Breast Cancer Vaccines Sponsors antigensPopulation) cancer DPX0907 Multipeptide ImmunoVaccine  7 58% 62% Tech.Multipeptide vaccine University of  5 22% 31% VirginiaAd-sig-hMUC-1/ecdCD40L Singapore CRI  1 91% 80% NY-ESO-1 IDC-G305 ImmuneDesign  1 84% 84% Corp. 6 HER2 peptide pulsed DC University  1 29% 36%Pennsylvania HER-2 B Cell peptide Ohio State  1 18% 23% UniversityHER-2/neu ID protein University  1 10% 11% Washington NeuVax peptideGalena Biopharma  1  6%  3% StimuVax ®(L-BLP25) peptide EMD Serono  1 6%  8% PolyPEPI915 Treos Bio 10 96% 93% *Proportion of subjects with ≥1PEPI3+

Another improvement of using the PolyPEPI915 vaccine is the lower chanceof tumor escape. Each 30 mer peptide in PolyPEPI915 targets 2 tumorantigens. CTLs against more tumor antigens are more effective againstheterologous tumor cells that CTLs against a single tumor antigen.

Another improvement is that PolyPEPI915 vaccine is that individuals wholikely respond to vaccination can be identified based on their HLAgenotypes (sequence) and optionally antigen expression in their tumorusing the methods described here. Pharmaceutical compositions withPolyPEPI vaccines will not be administered to individuals whose HLAcannot present any PEPI3 from the vaccines. During clinical trialscorrelation will be made between the mAGP or number of AGP in thePolyPEPI915 regimen and the duration of individual's responses. Avaccine combination with >1 AGP is most likely required to destroyheterologous tumor cells.

Example 20 Colorectal Cancer Vaccine Design and Composition

We show another example for colorectal vaccine composition using thesame design method demonstrated above. We used the PEPI3+ Test describedabove to design peptides for use in colorectal cancer vaccines that areeffective in a large percentage of patients, taking into account theheterogeneities of both tumour antigens and patient HLAs.

Colorectal cancer CTAs were identified and ranked based on the overallexpression frequencies of antigens found in colorectal cancer tumorsamples as reported in peer reviewed publications (FIG. 19) (Choi J,Chang H. The expression of MAGE and SSX, and correlation of COX2, VEGF,and survivin in colorectal cancer. Anticancer Res 2012. 32(2):559-564.;Goossens-Beumer I J, Zeestraten E C, Benard A, Christen T, Reimers M S,Keijzer R, Sier C F, Liefers G J, Morreau H, Putter H, Vahrmeijer A L,van de Velde C J, Kuppen P J. Clinical prognostic value of combinedanalysis of Aldh1, Survivin, and EpCAM expression in colorectal cancer.Br J Cancer 2014. 110(12):2935-2944.; Li M, Yuan Y H, Han Y, Liu Y X,Yan L, Wang Y, Gu J. Expression profile of cancer-testis genes in 121human colorectal cancer tissue and adjacent normal tissue. ClinicalCancer Res 2005. 11(5):1809-1814).

For the selection of the most frequently expressed colorectal cancerCTAs we used the PEPI3+ Test and the Model Population described inExample 8 to identify the “bestEPIs”.

We multiplied the reported expression frequency for each CTA (N %) bythe frequency of the PEPI3+ hotspots in the Model Population (B %) toidentify the T cell epitopes (9 mers) that will induce an immuneresponse against colorectal cancer antigens in the highest proportion ofindividuals (Table 33). We then selected 15 mers encompassing each ofthe selected 9 mers (Table 33). The 15 mers were selected to bind tomost HLA class II alleles of most subjects, using the process describedin Example 22 below. These 15 mers can induce both CTL and T helperresponses in the highest proportion of subjects.

TABLE 33 BestEPI list for selecting colorectal cancer peptidevaccine composition. Ntotal: number of biopsy samples(tumor specific antigen expression in human colorectalcancer tissues) analyzed for the expression of thecertain antigen; N+: number of individuals expressingthe certain antigen; N %: expression frequency of thecertain antigen; B %: bestEPI frequency, ie. thepercentage of induviduals having the bestEPI withinthe model population; N % * B %: expression frequencymultiplied by the bestEPI frequency. Antigen Information BestEPIs GeneLEN Ntotal N+ N % SEQ POS B % N % * B % TSP50 385 95 85 89% FSYEQDPTL106 51% 45.7% (SEQ ID NO: 21) EpCAM 314 309 273 88% RTYWIIIEL 140 51%45.1% (SEQ ID NO: 22) TSP50 385 95 85 89% TTMETQFPV 85 36% 32.6% (SEQ IDNO: 23) Spag9 1321 78 58 74% FSFVRITAL 1143 44% 32.6% (SEQ ID NO: 24)Spag9 1321 78 58 74% KMSSLLPTM 964 43% 32.1% (SEQ ID NO: 25) CAGE1 77747 35 74% KMHSLLALM 616 42% 31.5% (SEQ ID NO: 26) FBXO9 442 57 22 39%FMNPYNAVL 96 78% 30.1% (SEQ ID NO: 27) CAGE1 777 47 35 74% KSMTMMPAL 76037% 27.3% (SEQ ID NO: 28) EpCAM 314 309 273 88% YVDEKAPEF 251 28% 24.7%(SEQ ID NO: 29) FBXO39 442 57 22 39% KTMSTFHNL 218 58% 22.2% (SEQ IDNO: 30) Survivin 142 309 267 86% RAI EQ LAN 133 26% 22.2% (SEQ IDNO: 31) Spag9 1321 78 58 74% VMSERVSGL 19 28% 21.0% (SEQ ID NO: 32)TSP50 385 95 85 89% YRAQRFWSW 192 20% 17.8% (SEQ ID NO: 33) FBXO39 44257 22 39% FFFERIMKY 287 46% 17.6% (SEQ ID NO: 34) Survivin 142 309 26786% STFKNWPFL 20 15% 13.0% (SEQ ID NO: 35) Mage-A8 318 80 35 44%AIWEALSVM 223 20%  8.7% (SEQ ID NO: 36) Mage-A8 318 80 35 44% KVAELVRFL115 18%  7.7% (SEQ ID NO: 37) Mage-A6 314 250 69 28% FVQENYLEY 250 27% 7.5% (SEQ ID NO: 38) Mage-A8 318 80 35 44% RALAETSYV 279 16%  7.1%(SEQ ID NO: 39) Mage-A6 314 250 69 28% YIFATCLGL 176 25%  6.9% (SEQ IDNO: 40)

Then we designed 31 30 mer peptides. Each consist of two optimized 15mer fragments, generally from different frequent CTAs, where the 15 merfragments are arranged end to end, each fragment comprising one of the 9mers (BestEPIs) described above. Nine of these 30 mer peptides wereselected for a panel of peptide vaccines, referred to as PolyPEPI1015(Table 34). Expression frequencies for the 8 CTAs targeted byPolyPEPI1015, singly and in combination, are shown in FIG. 19.

TABLE 34 Selected Colorectal Cancer Vaccine peptides for PolyPEPI1015composition HLAI* HLAII** TREOSID Source Antigen Peptide(30mer) (CD8)(CD4) CCV1000-5-1 TSP50 PSTTMETQFPVSEGKSRYRAQRFWSWVGQA 53% 53%(SEQ ID NO: 90) CCV1000-2-2 EpCAM/SurvivinVRTYWIIIELKHKARTAKKVRRAIEQLAAM 57% 98% (SEQ ID NO: 81) CCV1000-5-3EpCAM/Mage-A8 YVDEKAPEFSMQGLKDEKVAELVRFLLRKY 43% 72% (SEQ ID NO: 91)CCV1000-5-4 TSP50/5pag9 RSCGESYEQDPILRDGIGKLGESEVRITAL 67% 82%(SEQ ID NO: 92) CCV1000-5-5 Mage-A8/Mage-A6SRAPEEAIWEALSVMQYFVQENYLEYRQVP 45% 76% (SEQ ID NO: 93) CCV1000-2-6CAGE1/Survivin LASKMHSLLALMVGLKDHRISTFKNWPFLE 58% 95% (SEQ ID NO: 84)CCV1000-5-7 CAGE1/Spag9 PKSMTMMPALFKENRSGAVMSERVSGLAGS 57% 57%(SEQ ID NO: 94) CCV1000-2-8 FBXO39 KFMNPYNAVLIKKFQKVNEFFERIMKYERL 90%98% (SEQID NO: 86) CCV1000-2-9 Spag9/FBXO39AQKMSSLLPTMWLGAFKKTMSTFHNLVSLN 67% 66% (SEQ ID NO: 87)PolyPEPI1015 (9 peptide together)  100%  99% *Percentage of individualshaving CD8+ T cell specific PEPI3+ within the Model Population (n= 433). **Percentage of individuals having CD4+ T cell specificPEPI4+ within the Model Population (n = 433).

Characterization of PolyPEPI1015 Colorectal Cancer Vaccine

Tumor heterogeneity: The PolyPEPI1015 composition targets 8 differentCTAs (FIG. 19). Based on the antigen expression rates for these 8 CTAs,AG50=5.22 and AG95=3 (FIGS. 20A-B). Patient heterogeneity: the AP50=4.73and AP95=2 (AP95=2) (FIGS. 21A-B). Both tumor and patient heterogeneity:AGP50=3.16 and AGP95=1 (Model Population) (FIGS. 22A-B).

Example 21—Comparison of Colorectal Cancer Vaccine Peptides withCompeting Colorectal Cancer Vaccines

We used the in silico clinical trial model described above to determineT cell responder rate of state of art and currently developed CRCpeptide vaccines and compared to that of polyPEPI1015 (Table 34). OurPEPI3+ test demonstrates that competing vaccines can induce immuneresponses against one tumor antigen in a fraction of subjects (2%-77%).However, the multi-antigen (multi-PEPI) response determination for the 2competitor multi-antigen vaccines resulted in no or 2% responders. *% ofresponders are the ratio of subjects from the Model population with1≥PEPI3+ for HLAI (CD8+ T cell responses) in case of 1, or for 2, 3, 4or 5 antigens of the vaccine compositions. Since multi-PEPI responsescorrelate with clinical responses induced by tumor vaccines, it isunlikely that any of the competing vaccines will demonstrate clinicalbenefit in 98% of patients. In contrast, we predicted multi-PEPIresponses in 95% of subjects suggesting the likelihood for clinicalbenefit in the majority of patients.

TABLE 35 Predicted immune response rates of polyPEPI1015 and competingcolorectal cancer vaccines % of CD8+ T cell responders in 433 subjects*Vaccine Colorectal Cancer antigens % responders against multiple AgsVaccines Sponsor (Ags) 1 Ag 2 Ags 3 Ags 4 Ags 5 Ags Stimuvax ® JohannesGutenberg 1  6% — — — — (L-BLP25) Peptide University Mainz Vaccine WT1Multipeptide Shinshu University, 1  79% — — — — Vaccine JapanMultiepitope Peptide Kinki University 7  5%  2%  0%  0%  0% CocktailVaccine p53 Synthetic Long Leiden University 1  77% — — — — PeptideVaccine Medical Center HER-2 B Cell Ohio State University 1  18% — — — —Peptide Vaccine Comprehensive Cancer Center NY-ESO-1 peptide Jonsson 1 0% — — — — pulsed dendritic cell ComprehensiveCancer vaccine CenterOCV-C02 Otsuka 2  2%  0% — — — Pharmaceutical Co., Ltd. TroVax vaccineOxford BioMedica 1  94% — — — — (OXB-301) ImMucin Vaxil Bio Theapeutics1  95% — — — — PolyPEPI 1015 Treos Bio 8 100% 95% 87% 70% 54%

Example 22. Efficacy by Design Procedure Exemplified for PolyPEPI1018Colorectal Cancer Vaccine

The PolyPEPI1018 Colorectal Cancer (CRC) Vaccine (PolyPEPI1018)composition is a peptide vaccine intended to be used as an add-onimmunotherapy to standard-of-care CRC treatment options in patientsidentified as likely responders using a companion in vitro diagnostictest (CDx). Clinical trials are ongoing in the US and Italy to evaluatePolyPEPI1018 in metastatic colorectal cancer patients. The productcontains 6 peptides (6 of the 30 mer peptides PolyPEPI1015 described inexamples 18 to 20 mixed with the adjuvant Montanide. The 6 peptides wereselected to induce T cell responses against 12 epitopes from 7 cancertestis antigens (CTAs) that are most frequently expressed in CRC. The 6peptides were optimized to induce long lasting CRC specific T cellresponses. Likely responder patients with T cell responses againstmultiple CTAs expressed in the tumor can be selected with a companiondiagnostic (CDx). This example sets out the precision process used todesign PolyPEPI1018. This process can be applied to design vaccinesagainst other cancers and diseases.

A. Selection of Multiple Antigen Targets

The selection of tumor antigens is essential for the safety and efficacyof cancer vaccines. The feature of a good antigen is to have restrictedexpression in normal tissues so that autoimmunity is prevented. Severalcategories of antigen meet this requirement, including uniquely mutatedantigens (e.g. p53), viral antigens (e.g. human papillomavirus antigensin cervical cancer), and differentiation antigens (e.g. CD20 in B-celllymphoma).

The inventors selected multiple cancer testis antigens (CTAs) as targetantigens since they are expressed in various types of tumor cells andtestis cells, but not expressed in any other normal somatic tissues orcells. CTAs are desirable targets for vaccines for at least thefollowing reasons:

-   -   tumors of higher histological grade and later clinical stage        often show higher frequency of CTA expression    -   only a subpopulation of tumor cells express a certain CTA    -   different cancer types are significantly different in their        frequency of CTA expression    -   tumors that are positive for a CTA often show simultaneous        expression of more than one CTA    -   None of the CTAs appear to be cell surface antigens, therefore        these are unique targets for cancer vaccines (they are not        suitable targets for antibody based immunotherapies)

To identify the target CTAs for PolyPEPI1018, the inventors built a CTAexpression knowledgebase. This knowledgebase contains CTAs that areexpressed in CRC ranked in order by expression rate. Correlation studiesconducted by the inventors (see Example 11) suggest that vaccines whichinduce CTL responses against multiple antigens that are expressed intumor cells can benefit patients. Therefore, seven CTAs with highexpression rates in CRC were selected for inclusion in PolyPEPI1018development. Details are set out in Table 36.

TABLE 36 Target CTAs in PolyPEPI1018 CRC vaccine Expression CTA NameRate Characterization TSP50 89.47% Testis-Specific Protease-Like Protein50 is an oncogene which induces cell proliferation, cell invasion, andtumor growth. It is frequently expressed in gastric-, breast-, cervical-and colorectal cancer samples; and rarely expressed in normal humantissues, except in spermatocytes of testes. EpCAM 88.35% Epithelial CellAdhesion Molecule is a tumor associated antigen, which is expressed incolon cancers and over-expressed in various human carcinomas. The highexpression of EpCAM in cancer-initiating stem cells makes it a valuabletarget for cancer vaccines. EpCAM is also expressed in at low ornegligible levels in normal epithelial cells, with the exception ofsquamous epithelium, hepatocytes and keratinocytes. Survivin 87.28%Survivin (Baculoviral IAP repeat-containing protein 5) is amulti-tasking protein that promotes cell proliferation and inhibitsapoptosis. Though it is strongly expressed in fetal tissues andnecessary for normal development, it is not expressed in most adulttissues. Survivin is expressed in various cancers including carcinomas.Normal tissues that express low level survivin include thymus, CD34⁺bone-marrow-derived stem cells, and basal colonic epithelium. Dramaticover-expression of survivin compared with normal tissues iis observed intumors in the lung, breast, colon, stomach, esophagus, pancreas,bladder, uterus, ovaries, large-cell non-Hodgkin's lymphoma, leukemias,neuroblastoma, melanoma and non-melanoma skin cancers. CAGE1 74.47%Cancer-associated gene 1 protein is a typical CTA, which might play arole in cell proliferation and tumorigenesis. CAGE1 is highly expressedin colorectal cancer tissues and weakly expressed in adjacent normalcolorectal mucosa. In addition, CAGE1 is expressed in melanoma,hepatoma, and breast tumors. No CAGE1 protein expression is detected inhealthy human tissues, other than testes. SPAG9 74.36% Sperm-associatedantigen 9 is involved in c-Jun N-terminal kinase-signaling and functionsas a scaffold protein, thus playing an important role in cell survival,proliferation, apoptosis and tumor development. SPAG9 expression wasdetected in epithelial ovarian cancer (90%), breast cancer (88%),cervical cancer (82%), renal cell cancer (88%) and colorectal cancer(74%) patients. None of the adjacent noncancerous tissues showed antigenexpression. SPAG9 expression is restricted to testis. FBXO39 38.60%FBXO39 (BCP-20) is a testis specific protein and is an important part ofthe E3 ubiquitin ligase complex. It participates in ubiquitination andhas a role in regulating the cell cycle, immune responses, signaling,and proteasomal degradation of proteins. FBXO39 is expressed in colonand breast cancers. FBXO39 expression has also been detected in ovary,placenta, and lung. FBXO39 expression is 100-fold higher in testis and1,000-fold higher in colorectal cancers compared with normal tissue.MAGEA8 43.75% Melanoma-associated antigen 8 function is not known,though it may play a role in embryonal development and tumortransformation or aspects of tumor progression. MAGE-A8 gene isexpressed in CRC and hepatocellular carcinoma. MAGE-A8 expression innormal tissues is restricted to the testis and the placenta. B. PreciseTargeting is Achieved by PEPI3+ Biomarker Based Vaccine Design

As described above the PEPI3+ biomarker predicts a subject's vaccineinduced T cell responses. The inventors developed and validated a testto accurately identify the PEPIs from antigen sequences and HLAgenotypes (Examples 1, 2, 3). The PEPI Test algorithm was used toidentify the dominant PEPIs (bestEPIs) from the 7 target CTAs to beincluded in PolyPEPI1018 CRC vaccine.

The dominant PEPIs identified with the process described here can induceCTL responses in the highest proportion of subjects:

-   -   i. Identification of all HLA class I binding PEPIs from the 7        CTA targets in each of the 433 subjects in the Model Population    -   ii. Identification of the dominant PEPIs (BestEPIs) that are        PEPIs present in the largest subpopulation.

The 12 dominant PEPIs that are derived from the 7 CTAs in PolyPEPI1018are presented in the following table. The PEPI % in Model Populationindicates the proportion of 433 subjects with the indicated PEPI, i.e.the proportion of subjects where the indicated PEPI can induce CTLresponses. There is very high variability (18%-78%) in the dominantPEPIs to induce CTL responses despite the optimization steps used in theidentification process.

TABLE 37 CRC specific HLA class I binding dominant PEPIs in PolyPEPI1018Dominant PEPI3+ for each of the 7 CTAs in PolyPEPI1018 in CRC patientsPEPI3+ % in SEQ Peptides in CRC Dominant Model ID PolyPEPI1018  AntigensPEPI3+ Population NO: CRC-P1 TSP50 TTMETQFPV 36% 23 YRAQRFWSW 20% 33CRC-P2 EpCAM RTYWIIIEL 51% 22 Survivin RAIEQLAAM 26% 31 CRC-P3 EpCAMYVDEKAPEF 28% 29 MAGE-A8 KVAELVRFL 18% 37 CRC-P6 CAGE1 KMHSLLALM 42% 26Survivin STFKNWPFL 15% 35 CRC-P7 CAGE1 KSMTMMPAL 37% 28 SPAG9 VMSERVSGL28% 32 CRC-P8 FBXO39 FMNPYNAVL 78% 27 FFFERIMKY 46% 34

The inventors optimized each dominant PEPI to bind to most HLA class IIalleles of most subjects. This should enhance efficacy, because it willinduce CD4+ T helper cells that can augment CD8+ CTL responses andcontribute to long lasting T cell responses. The example presented inFIG. 4 demonstrates that PEPIs that bind to 3 HLA class II alleles mostlikely activate T helper cells.

The 15-mer peptides selected with the process described here containboth HLA class I and class II binding dominant PEPIs. Therefore, thesepeptides can induce both CTL and T helper responses in the highestproportion of subjects.

Process:

-   -   1. Identification the HLA class II genotype of 400 normal        donors*    -   2. Extension of each 9-mer dominant PEPI (Table 33) on both        sides with amino acids that match the source antigen    -   3. Prediction of HLA class II PEPIs of 400 normal donors using        an IEDB algorithm    -   4. Selection the 15-mer peptide with the highest proportion of        subject have HLA Class II binding PEPIs    -   5. Ensure the presence of one dominant HLA class II PEPI in each        vaccine peptide when joining two 15-mer peptides

The 12 optimized 15-mer peptides derived from the 7 CTAs in PolyPEPI1018are presented in the Table 38. These peptides have different HLA classII binding characteristics. There is a high variability (0%-100%) inPEPI generation capacity (3 HLA binding) among these peptides despitesuch an optimized personalized vaccine design.

TABLE 38 Antigen specific HLA class II binding PEPIs in PolyPEPI1018. %% % % Average subjects subjects subjects subjects HLA with ≥ with ≥ with≥ with ≥ class II 1 HLA 2 HLA 3 HLA 4 HLA CRC binding class II class IIclass II class II Nr. antigens alleles binding binding binding bindingCRC-P1 TSP50 0  0%  0%  0%  0% (83-97) TSP50 4 100%  99%  88%  53%(190-204) CRC-P2 EPCAM 5 100% 100% 100%  98% (139-153) SURVIVIN 2  84% 58%  26%  11% (127-141) CRC-P3 EPCAM 0  0%  0%  0%  0% (251-265)MAGE-A8 4 100% 100%  95%  72% (113-127) CRC-P6 CAGE 5 100% 100%  99% 95% (613-627) SURVIVIN 3 100%  97%  83%  45% (15-29) CRC-P7 CAGE 3 100% 98%  87%  56% (759-773) SPAG9 1  66%  35%  9%  2% (16-30) CRC-P8 FBXO393 100%  94%  43%  13% (95-109) FBXO39 5 100% 100% 100%  98% (284-298)

The 30-mer vaccine peptides have the following advantages compared toshorter peptides:

-   -   (i) Multiple precisely selected tumor specific immunogens: each        30 mer contains two precisely selected cancer specific        immunogenic peptides that are capable to induce CTL and T helper        responses in the majority of the relevant population (similar to        the model population).    -   (ii) Ensure natural antigen presentation. 30-mer long        polypeptides can be viewed as pro-drugs: They are not        biologically active by themselves, but are processed to smaller        peptides (9 to 15 amino acid long) to be loaded into the HLA        molecules of professional antigen presenting cells. The antigen        presentation resulting from long peptide vaccination reflects        physiological pathways for presentation in both HLA class I and        class II molecules. In addition, long peptide processing in the        cells is much more efficient than that of large intact proteins.    -   (iii) Exclude induction of tolerizing T cell responses. 9-mer        peptides do not require processing by professional        antigen-presenting cells and therefore bind exogenously to the        HLA class I molecules. Thus, injected short peptides will bind        in large numbers to HLA class I molecules of all nucleated cells        that have surface HLA class I. In contrast, >20-mers long        peptides are processed by antigen presenting cells before        binding to HLA class I. Therefore, vaccination with long        peptides is less likely to lead to tolerance and will promote        the desired antitumor activity.    -   (iv) Induce long lasting T cell responses because it can        stimulate T helper responses by binding to multiple HLA class II        molecules    -   (v) Utility. GMP manufacturing, formulation, quality control and        administration of a smaller number of peptides (each with all of        the above characteristics) is more feasible than a larger number        of peptides supplying different characteristics.

Each 30-mer peptide in PolyPEPI1018 consists of 2 HLA class I bindingdominant PEPIs and at least one strong HLA class II binding PEPI. Strongbinding PEPIs bind to 4 HLA class II alleles in >50% of individuals.Therefore, the vaccine peptides are tailored to both HLA class I andclass II alleles of individual subjects in a general population (whichis a relevant population for CRC vaccine design).

As demonstrated above the high HLA genotype variability in subjectsresults in high variability of T cell responses induced by PolyPEPI1018.This justifies the co-development of a CDx that determines likelyresponders. The PEPI3+ and >2PEPI3+ biomarkers could predict the immuneresponse and clinical responses, respectively, of subjects vaccinatedwith PolyPEPI1018 as detailed in Examples 11 and 12. These biomarkerswill be used to co-develop a CDx which predicts likely responders toPolyPEPI1018 CRC vaccine.

Example 23—Analysis of the Composition and Immunogenicity ofPolyPEPI1018 CRC Vaccine

Selected peptides for the PolyPEPI1018 composition are as shown in Table39.

TABLE 39Selected Colorectal Cancer Vaccine peptides for PolyPEPI1018 compositionHLAI* HLAII** SEQID TREOSID Source Antigen Peptide (30mer) (CD8) (CD4)90 CCV1000-5-1 TSP50 PSTTMETQFPVSEGKSRYRAQRFWSWVGQA 53%  88% 81CCV1000-2-2 EpCAM/Survivin VRTYWIIIELKHKARTAKKVRRAIEQLAAM 57% 100% 91CCV1000-5-3 EpCAM/Mage-A8 YVDEKAPEFSMQGLKDEKVAELVRFLLRKY 43%  95% 84CCV1000-2-6 Cage/Survivin LASKMHSLLALMVGLKDHRISTFKNWPFLE 58%  99% 94CCV1000-5-7 Cage/Spag9 PKSMTMMPALFKENRSGAVMSERVSGLAGS 57%  87% 86CCV1000-2-8 FBXO39 KFMNPYNAVLTKKFQKVNFFFERIMKYERL 90% 100%PolyPEPI1018 (6 peptide together) 98% 100% *Percentage of individualshaving CD8+ T cell specific PEPI3+ within the Model Population (n= 433). **Percentage of individuals having CD4+ T cell specificPEPI4+ within normal donors (n = 400).

Characterization of Immunogenicity

The inventors used the PEPI3+ Test to characterized the immunogenicityof PolyPEPI1018 in a cohort of 37 CRC patients with complete HLAgenotype data. T cell responses were predicted in each patient againstthe same 9 mer peptides that will be used in clinical trials. Thesepeptides represent the 12 dominant PEPI3+ within the PolyPEPI1018peptides. The 9 mers are shown in Table 39.

The specificity and sensitivity of PEPI3+ prediction depends on theactual number of HLAs predicted to bind a particular epitope.Specifically, the inventors have determined that the probability thatone HLA-restricted epitope induces a T cell response in a subject istypically 4%, which explains the poor sensitivity of the state-of-artprediction methods based on HLA restricted epitope prediction. Applyingthe PEPI3+ methodology, the inventors determined the probability that Tcell response to each of the dominant PEPI3+-specific would be inducedby PolyPEPI1018 in the 37 CRC patients. The results from this analysisare summarized in the Table 40.

TABLE 40 Probability of Dominant PEPI in the 6 Peptides of PolyPEPI1018in 37 CRC Patients CRC-P1 CRC-P2 CRC -P3 CRC-P6 CRC-P7 CRC-P8 TSP50TSP50 EpCAM Survivin EpCAM MAGEA8 CAGE1 Survivin CAGE1 SPAG9 FBXO39FBXO39 Expected CRC (83- (190- (139- (127- (251- (113- (613- (15- (759-(16- (95- (284- Number Patient 97) 204) 153) 141) 265) 127) 627) 29)773) 30) 109) 298) of PEPIs CRC-01 22%  4% 22%  4% 22% 22% 100%  1% 98%84% 100% 22% 5.01 CRC-02 22%  1% 22% 22% 22% 22% 100%  1% 98% 22% 100%98% 5.29 CRC-03 84% 22% 84% 22% 22% 22%  84% 22% 22% 22% 100% 22% 5.29CRC-04 22% 84% 22%  4% 22%  4%  98%  4%  4% 22% 100% 84% 4.70 CRC-05 22%22%  4%  4% 22%  4%  98%  1%  4%  4% 100% 84% 3.68 CRC-06 84% 22%  4%84% 98%  4%  22%  4%  4%  4% 100% 98% 5.27 CRC-07 22% 22% 22% 22% 22% 4%  98%  1% 22% 22% 100% 84% 4.41 CRC-08 22% 22% 22% 98% 84% 22%  84%22% 22% 22% 100% 84% 6.04 CRC-09 22% 84% 84% 84% 84% 22% 100%  4% 22%22%  98% 84% 7.10 CRC-10  4% 98% 22% 22%  4%  4%  4% 22% 22% 22%  98%84% 4.06 CRC-11 22% 22%  4%  4% 22%  4%  84%  1%  4%  4%  98% 84% 3.53CRC-12 84% 22%  4% 22%  4%  4%  84%  4% 84%  4% 100% 22% 4.38 CRC-13 84%22%  4% 22% 84%  4%  84%  1%  1%  4% 100% 98% 5.07 CRC-14 22% 84%  4% 4% 22%  4%  84%  1%  4%  4% 100% 84% 4.16 CRC-15 84% 22% 22% 22% 22% 4%  84%  4% 22%  4% 100% 84% 4.74 CRC-16  4% 84%  4%  4% 22%  4%  84% 1%  4% 22% 100% 84% 4.16 CRC-17 84% 84%  4% 84% 84%  4%  4%  4%  4%  4%100% 22% 4.82 CRC-18 84% 22% 22% 84% 84%  4%  22% 22%  4%  4% 100% 84%5.36 CRC-19 22% 22% 22% 22% 22%  4%  98%  4% 22% 22% 100% 84% 4.45CRC-20 84% 22%  4% 22% 84%  4%  84%  1%  4%  4% 100% 98% 5.10 CRC-21 22%22% 22% 22% 84% 22%  98%  4%  4% 22% 100% 84% 5.06 CRC-22 22% 98% 84% 4% 22% 22%  84% 22% 84% 22%  98% 22% 5.84 CRC-23 84% 84% 84% 84% 84%22%  84% 84% 84%  4% 100% 84% 8.82 CRC-24 22% 22%  4%  4% 22%  4%  84% 1%  4%  4% 100% 84% 3.55 CRC-25 22% 84% 22%  4% 22%  4%  84%  4% 22% 4% 100% 84% 4.56 CRC-26 84% 22%  4% 22% 84%  4%  84%  1%  4%  4% 100%84% 4.97 CRC-27 22% 22%  4%  4% 22%  4%  98%  1%  4%  4% 100% 84% 3.68CRC-28 84% 22%  4% 22% 84%  4%  84%  1%  4%  4% 100% 98% 5.10 CRC-29 84%84%  4% 22% 22%  4%  84%  1% 22% 22% 100% 84% 5.33 CRC-30 84% 22%  4%22% 84%  4%  84%  1%  4%  4% 100% 98% 5.10 CRC-31 22% 84% 22%  4%  4% 4%  22%  1%  4%  4%  98% 84% 3.53 CRC-32 84% 84%  4% 84% 22%  4%  4% 4%  4%  4%  98% 84% 4.80 CRC-33 84% 22%  4% 22% 84%  4%  84%  1%  4% 4% 100% 98% 5.10 CRC-34 22% 22% 22% 22% 22%  4%  84%  1% 22%  4% 100%84% 4.09 CRC-35 22%  4%  4%  1% 22%  4%  4%  1%  4%  4%  84% 84% 2.37CRC-36 22%  4%  4%  1% 22%  4%  4%  1%  4%  4%  84% 84% 2.37 CRC-37 22% 4%  4%  1% 22%  4%  4%  1%  4%  4%  84% 84% 2.37 Abbreviations: CRC =colorectal cancer; PEPI = personal epitope Note: Percentages representthe likelihood of CD8+ T cell Responses Induced by PolyPEPI1018.

Overall, these results show that the most immunogenic peptide inPolyPEPI1018 is CRC-P8, which it is predicted to bind to >3 HLAs in mostpatients. The least immunogenic peptide, CRC-P3, binds to >1 HLA in manypatients and has a 22% chance of inducing T cell responses. Sincebioassays used to detect T cell responses are less accurate than PEPI3+,this calculation may be the most accurate characterization of the T cellresponses in CRC patients. Though MAGE-A8 and SPAG9 were immunogenic inthe Model Population used for vaccine design, MAGE-A8-specific PEPI3+were absent in the 37 CRC patients, and only one patient (3%) had SPAG9specific PEPI3+.

Characterization of Toxicity—immunoBLAST

A method was developed that can be performed on any antigen to determineits potential to induce toxic immune reaction, like autoimmunity. Themethod is referred to herein as immunoBLAST. PolyPEPI1018 contains six30-mer polypeptides. Each polypeptide consists of two 15-mer peptidefragments derived from antigens expressed in CRC. Neoepitopes might begenerated in the joint region of the two 15-mer peptides and couldinduce undesired T cell responses against healthy cells (autoimmunity).This was assesses using the inventors applied the immunoBLASTmethodology.

A 16-mer peptide for each of the 30-mer components of PolyPEP1018 wasdesigned. Each 16-mer contains 8 amino acids from the end of the first15 residues of the 30-mer and 8 amino acids from the beginning of thesecond 15 residues of the 30-mer—thus precisely spanning the jointregion of the two 15-mers. These 16-mers are then analysed to identifycross-reactive regions of local similarity with human sequences usingBLAST(https://blast.ncbi.nlm.nih.gov/Blast.cgi), which compares proteinsequences to sequence databases and calculates the statisticalsignificance of matches. 8-mers within the 16-mers were selected as theexamination length since that length represents the minimum lengthneeded for a peptide to form an epitope, and is the distance between theanchor points during HLA binding.

As shown in FIG. 23, the positions of amino acids in a polypeptide arenumbered. The start positions of potential 9-mer peptides that can bindto HLAs and form neoepitopes are the 8 amino acids in positions 8-15.The start positions of tumor antigen derived peptides harbored by the15-mers that can form the pharmaceutically active epitopes are 7+7=14amino acids at position 1-7 and 16-22. The ratio of possible neoepitopegenerating peptides is 36.4% (8/22).

The PEPI3+ Test was used to identify neoepitopes and neoPEPI among the9-mer epitopes in the joint region. The risk of PolyPEPI1018 inducingunwanted T cell responses was assessed in the 433 subjects in the ModelPopulation by determining the proportion of subjects with PEPI3+ amongthe 9-mers in the joint region. The result of neoepitope/neoPEPIanalysis is summarized in table 41. In the 433 subjects of the ModelPopulation, the average predicted epitope number that could be generatedby intracellular processing was 40.12. Neoepitopes were frequentlygenerated; 11.61 out of 40.12 (28.9%) epitopes are neoepitopes. Most ofthe peptides were able to be identified as a neoepitope, but the numberof subjects that present neoepitopes varied.

Epitopes harbored by PolyPEPI1018 create an average of 5.21 PEPI3+.These PEPIs can activate T cells in a subject. The amount of potentialneoPEPIs was much lower than neoepitopes (3.7%). There is a marginalpossibility that these neoPEPIs compete on T cell activation with PEPIsin some subjects. Importantly, the activated neoPEPI specific T cellshad no targets on healthy tissue.

TABLE 41 Identification of Potential Neoepitopes of PolyPEPI1018Epitope & PEPI3+ binding in 433 Subjects of the Model PopulationPolyPEPI1 Epitope Binding PEPI3+ binding 018 (1 × HLA) (3 × HLA) PeptidePotential NeoEPI NeoPEPI ID: Neoepitope Sub# Sub % NeoEPI count Sub#Sub % NeoPEPI count CRC-P1 QFPVSEGKS 0  0.0% 7 0 0.0% 3 (SEQ ID NO: 141)FPVSEGKSR 160 37.0% X 1 0.2% X (SEQ ID NO: 142) PVSEGKSRY 150 34.6% X 00.0% (SEQ ID NO: 143) VSEGKSRYR 194 44.8% X 1 0.2% X SEQ ID NO: 144)SEGKSRYRA 113 26.1% X 0 0.0% (SEQ ID NO: 145) EGKSRYRAQ 77 17.8% X 00.0% (SEQ ID NO: 146) GKSRYRAQR 37  8.5% X 0 0.0% (SEQ ID NO: 147)KSRYRAQRF 337 77.8% X 33 7.6% X (SEQ ID NO: 148) CRC-P2 IELKHKART 32 7.4% X 7 0 0.0% 1 (SEQ ID NO: 149) ELKHKARTA 63 14.5% X 0 0.0%(SEQ ID NO: 150) LKHKARTAK 59 13.6% X 0 0.0% (SEQ ID NO: 151) KHKARTAKK166 38.3% X 1 0.2% (SEQ ID NO: X 152) HKARTAKKV 0  0.0% 0 0.0%(SEQ ID NO: 153) KARTAKKVR 70 16.2% X 0 0.0% (SEQ ID NO: 154) ARTAKKVRR134 30.9% X 0 0.0% (SEQ ID NO: 155) RTAKKVRRA 41  9.5% X 0 0.0%(SEQ ID NO: 156) CRC-P3 EFSMQGLKD 0  0.0% 5 0 0.0% 1 (SEQ ID NO: 157)FSMQGLKDE 188 43.4% X 0 0.0% (SEQ ID NO: 158) SMQGLKDEK 138 31.9% X 00.0% (SEQ ID NO: 159) MQGLKDEKV 16  3.7% X 0 0.0% (SEQ ID NO: 160)QGLKDEKVA 0  0.0% 0 0.0% (SEQ ID NO: 161) GLKDEKVAE 0  0.0% 0 0.0%(SEQ ID NO: 162) LKDEKVAEL 186 43.0% X 3 0.7% X (SEQ ID NO: 163)KDEKVAELV 51 11.8% X 0 0.0% (SEQ ID NO: 164) CRC-P6 LLALMVGLK 252 58.2%X 7 0 0.0% 1 (SEQ ID NO: 165) LALMVGLKD 86 19.9% X 0 0.0% (SEQ ID NO:166) ALMVGLKDH 65 15.0% X 0 0.0% (SEQ ID NO: 167) LMVGLKDHR 97 22.4% X 00.0% (SEQ ID NO:   168) MVGLKDHRI 67 15.5% X 0 0.0% (SEQ ID NO: 169)VGLKDHRIS 0  0.0% 0 0.0% (SEQ ID NO: 170) GLKDHRIST 4  0.9% X 0 0.0%(SEQ ID NO: 171) LKDHRISTF 195 45.0% X 5 1.2% X (SEQ ID NO: 172) CRC-P7PALFKENRS 0  0.0% 5 0 0.0% 1 (SEQ ID NO: 173) ALFKENRSG 0  0.0% 0 0.0%(SEQ ID NO: 174) LFKENRSGA 41  9.5% X 0 0.0% (SEQ ID NO: 175) FKENRSGAV114 26.3% X 0 0.0% (SEQ ID NO: 176) KENRSGAVM 261 60.3% X 0 0.0%(SEQ ID NO: 177) ENRSGAVMS 0  0.0% 0 0.0% (SEQ ID NO: 178) NRSGAVMSE 22752.4% X 0 0.0% (SEQ ID NO: 179) RSGAVMSER 2 0.5% (SEQ ID NO: 197 45.5% XX 180) CRC-P8 AVLTKKFQK 181 41.8% X 7 0 0.0% 3 (SEQ ID NO: 181)VLTKKFQKV 208 48.0% X 2 0.5% X (SEQ ID NO: 182) LTKKFQKVN 0  0.0% 0 0.0%(SEQ ID NO: 183) TKKFQKVNF 25  5.8% X 0 0.0% (SEQ ID NO: 184) KKFQKVNFF250 57.7% X 12 2.8% X (SEQ ID NO: 185) KFQKVNFFF 273 63.0% X 23 5.3% X(SEQ ID NO: 186) FQKVNFFFE 163 37.6% X 0 0.0% (SEQ ID NO: 187) QKVNFFFER110 25.4% X 0 0.0% (SEQ ID NO: 188) Abbreviations: CRC = colorectalcancer; HLA = human leukocytic antigen; PEPI = personal epitope

Each of the 30-mer peptides in PolyPEPI1018 were released for clinicaldevelopment since none of the 8-mers in the joint regions matched anyhuman protein, except the target CTAs.

Characterisation of Activity/Efficacy

The inventors have developed pharmacodynamic biomarkers to predict theactivity/effect of vaccines in individual human subjects as well as inpopulations of human subjects. These biomarkers expedite more effectivevaccine development and also decrease the development cost. Theinventors have the following tools:

Antigen expression knowledgebase: The inventors have collected data fromexperiments published in peer reviewed scientific journals regarding thetumor antigens expressed by tumor cells and organized by tumor type tocreate a database of CTA expression levels—CTA database (CTADB). As ofApril 2017, the CTADB contained data from 145 CTAs from 41,132 tumorspecimens, and was organized by the CTA expression frequencies indifferent types of cancer. In silico trial populations: The inventorshave also collected data on the HLA genotypes of several different modelpopulations. Each individual in the populations has complete 4-digit HLAgenotype and ethnicity data. The populations are summarized in Table 42.

TABLE 42 In silico trial populations Number of Population SubjectsInclusion criteria Model Population 433 Complete HLA class I genotypeDiverse ethnicity CRC patients 37 Complete HLA class I genotype CRCdiagnosis, unknown ethnicity “Big” Population 7,189 Complete HLA class Igenotype Diverse ethnicity Chinese 234 Complete HLA class I genotypePopulation Chinese ethnicity Irish Population 999 Complete HLA class Igenotype Irish ethnicity Abbreviations: CRC = colorectal cancer; HLA =human leukocyte antigen

Using these tools (or potentially equivalent databases or modelpopulations), the following markers can be assessed:

-   -   AG95—potency of a vaccine: The number of antigens in a cancer        vaccine that a specific tumor type expresses with 95%        probability. AG95 is an indicator of the vaccine's potency, and        is independent of the immunogenicity of the vaccine antigens.        AG95 is calculated from the tumor antigen expression rate data,        which is collected in the CTADB. Technically, AG95 is determined        from the binomial distribution of CTAs, and takes into account        all possible variations and expression rates. In this study,        AG95 was calculated by cumulating the probabilities of a certain        number of expressed antigens, by the widest range of antigens        where the sum of probabilities was less than or equal to 95%.        The correct value is between 0 (no expression expected with 95%        probability) and maximum number of antigens (all antigens        expressed with 95% probability).    -   PEPI3+ count—immunogenicity of a vaccine in a subject:        Vaccine-derived PEPI3+ are personal epitopes that induce T cell        responses in a subject. PEPI3+ can be determined using the        PEPI3+ Test in subjects who's complete 4-digit HLA genotype is        known.    -   AP count—antigenicity of a vaccine in a subject: Number of        vaccine antigens with PEPI3+. Vaccines like PolyPEPI1018 contain        sequences from antigens expressed in tumor cells. AP count is        the number of antigens in the vaccine that contain PEPI3+, and        the AP count represents the number of antigens in the vaccine        that can induce T cell responses in a subject. AP count        characterizes the vaccine-antigen specific T cell responses of        the subject since it depends only on the HLA genotype of the        subject and is independent of the subject's disease, age, and        medication. The correct value is between 0 (no PEPI presented by        the antigen) and maximum number of antigens (all antigens        present PEPIs).    -   AP50—antigenicity of a vaccine in a population: The mean number        of vaccine antigens with a PEPI in a population. The AP50 is        suitable for the characterization of vaccine-antigen specific T        cell responses in a given population since it depends on the HLA        genotype of subjects in a population. Technically, the AP count        was calculated in the Model Population and the binomial        distribution of the result was used to calculate the AP50.    -   AGP count—effectiveness of a vaccine in a subject: Number of        vaccine antigens expressed in the tumor with PEPI. The AGP count        indicates the number of tumor antigens that vaccine recognizes        and induces a T cell response against (hit the target). The AGP        count depends on the vaccine-antigen expression rate in the        subject's tumor and the HLA genotype of the subject. The correct        value is between 0 (no PEPI presented by expressed antigen) and        maximum number of antigens (all antigens are expressed and        present a PEPI).    -   AGP50—effectiveness of a cancer vaccine in a population: The        mean number of vaccine antigens expressed in the indicated tumor        with PEPI (i.e., AGP) in a population. The AGP50 indicates the        mean number of tumor antigens that the T cell responses induced        by the vaccine can recognize. AGP50 is dependent on the        expression rate of the antigens in the indicated tumor type and        the immunogenicity of the antigens in the target population.        AGP50 can estimate a vaccine's effectiveness in different        populations and can be used to compare different vaccines in the        same population. The computation of AGP50 is similar to that        used for AG50, except the expression is weighted by the        occurrence of the PEPI3+ in the subject on the expressed vaccine        antigens. In a theoretical population, where each subject has a        PEPI from each vaccine antigen, the AGP50 will be equal to AG50.        In another theoretical population, where no subject has a PEPI        from any vaccine antigen, the AGP50 will be 0. In general, the        following statement is valid: 0≤AGP50≤AG50.    -   mAGP—a candidate biomarker for the selection of likely        responders: Likelihood that a cancer vaccine induces T cell        responses against multiple antigens expressed in the indicated        tumor. mAGP is calculated from the expression rates of        vaccine-antigens in CRC and the presence of vaccine derived        PEPIs in the subject. Technically, based on the AGP        distribution, the mAGP is the sum of probabilities of the        multiple AGP (≥2 AGPs).        Application of these Markers to Assess Antigenicity and        Effectiveness PolyPEPI1018 in Individual Patients with CRC

Table 43 shows the antigenicity and effectiveness of PolyPEPI1018 in 37CRC patients using AP and AGP50, respectively. As expected from the highvariability of PolyPEPI1018 specific T cell responses (see Table 41),the AP and AGP50 have high variability. The most immunogenic antigen inPolyPEPI1018 was FOX039; each patient had a PEPI3+. However, FOX039 isexpressed only 39% of CRC tumors, suggesting that 61% of patients willhave FOX039 specific T cell responses that do not recognize the tumor.The least immunogenic antigen was MAGE-A8; none of the 37 CRC patientshad a PEPI3+ despite the antigen being expressed in 44% of CRC tumors.These results illustrate that both expression and immunogenicity ofantigens can be taken into account when determining a cancer vaccine'seffectiveness.

AGP50 indicates the mean number of expressed antigens in CRC tumor withPEPIs. Patients with higher AGP50 values are more likely to respond toPolyPEPI1018 since higher AGP50 values indicate that the vaccine caninduce T cell responses against more antigens expressed in CRC cells.

The last column in the Table 43 shows the probability of mAGP (multipleAGP; i.e., at least 2 AGPs) in each of the 37 CRC patients. The averagemAGP in patients with CRC is 66%, suggesting that there is a 66%likelihood that a CRC patient will induce T cell responses againstmultiple antigens expressed in the tumor.

TABLE 43 Antigenicity (AP count), Effectiveness (AGP50 count), and mAGPof PolyPEPI1018 in 37 CRC Patients Antigens (CTAs) in PolyPEPI1018Number TSP50 EpCAM Survivin CAGE1 SPAG9 FBXO39 MAGE-A8 Number ofExpression rate of AGP50 89% 88% 87% 74% 74% 39% 44% AP (AP (AGP50 CRCPatients count) count) mAGP CRC-01 0 0 0 1 1 1 0 3 1.87 90% CRC-02 0 0 01 0 1 0 2 1.13 85% CRC-03 1 1 0 1 0 1 0 4 2.91 97% CRC-04 1 0 0 1 0 1 03 2.03 91% CRC-05 0 0 0 1 0 1 0 2 1.13 78% CRC-06 1 1 1 1 0 1 0 5 3.7899% CRC-07 0 0 0 1 0 1 0 2 1.13 84% CRC-08 0 1 1 1 0 1 0 4 2.89 98%CRC-09 1 1 1 1 0 1 0 5 3.78 99% CRC-10 1 0 0 0 0 1 0 2 1.28 86% CRC-11 00 0 1 0 1 0 2 1.13 79% CRC-12 1 0 0 1 0 1 0 3 2.03 88% CRC-13 1 1 1 1 01 0 5 3.78 98% CRC-14 1 0 0 1 0 1 0 3 2.03 87% CRC-15 1 0 0 1 0 1 0 32.03 90% CRC-16 1 0 0 1 0 1 0 3 2.03 85% CRC-17 1 1 1 0 0 1 0 4 3.04 96%CRC-18 1 1 1 1 0 1 0 5 3.78 98% CRC-19 0 0 0 1 0 1 0 2 1.13 85% CRC-20 11 1 1 0 1 0 5 3.78 98% CRC-21 0 1 0 1 0 1 0 3 2.01 93% CRC-22 1 1 0 1 01 0 4 2.91 97% CRC-23 1 1 1 1 0 1 0 5 3.78 99% CRC-24 0 0 0 1 0 1 0 21.13 82% CRC-25 1 0 0 1 0 1 0 3 2.03 89% CRC-26 1 1 0 1 0 1 0 4 2.91 95%CRC-27 0 0 0 1 0 1 0 2 1.13 78% CRC-28 1 1 1 1 0 1 0 5 3.78 98% CRC-29 10 0 1 0 1 0 3 2.03 92% CRC-30 1 1 1 1 0 1 0 5 3.78 98% CRC-31 1 0 0 0 01 0 2 1.28 80% CRC-32 1 0 1 0 0 1 0 3 2.15 91% CRC-33 1 1 1 1 0 1 0 53.78 98% CRC-34 0 0 0 1 0 1 0 2 1.13 82% CRC-35 0 0 0 0 0 1 0 1 0.39 55%CRC-36 0 0 0 0 0 1 0 1 0.39 55% CRC-37 0 0 0 0 0 1 0 1 0.39 55%Abbreviations: CRC = colorectal cancer; PEPI = personal epitope; CTA =cancer testis antigen; AP = expressed antigens with ≥ 1 PEPI

These biomarkers have immediate utility in vaccine development and inthe routine clinical practice because they do not require invasivebiopsies. Antigen expression data can be obtained from achieved tumorspecimen and organized in databases. 4-digit HLA genotyping can be donefrom a saliva specimen. It is a validated test performed by certifiedlaboratories worldwide for transplantation and paternity testing. Theseassessments will allow drug developers and physicians to gain deeperinsights into the immunogenicity and activity of tumor response and thepossible emergence of resistance.

Application of these Markers to Asses Antigenicity and EffectivenessPolyPEPI1018 in Populations

Antigenicity of PolyPEPI1018 CRC Vaccine in a General Population

The antigenicity of PolyPEPI1018 in a subject is determined by the APcount, which indicates the number of vaccine antigens that induce T cellresponses in a subject. The AP count of PolyPEPI1018 was determined ineach of the 433 subjects in the Model Population using the PEPI Test,and the AP50 count was then calculated for the Model Population.

As shown in FIG. 24 the AP50 of PolyPEPI1018 in the Model Population is3.62. Therefore, the mean number of immunogenic antigens (i.e., antigenswith ≥1 PEPI) in PolyPEPI1018 in a general population is 3.62.

Effectiveness of PolyPEPI1018 CRC Vaccine in a General Population

Vaccine induced T cells can recognize and kill tumor cells if a PEPI inthe vaccine is presented by the tumor cell. The number of AGPs(expressed antigens with PEPI) is an indicator of vaccine effectivenessin an individual, and is dependent on both the potency and antigenicityof PolyPEPI1018. As shown in FIG. 25, the mean number of immunogenicCTAs (i.e., AP [expressed antigens with ≥1 PEPI]) in PolyPEPI1018 is2.54 in the Model Population.

The likelihood that PolyPEPI1018 induces T cell responses againstmultiple antigens in a subject (i.e., mAGP) in the Model Population is77%.

Comparison of the PolyPEPI1018 CRC Vaccine Activities in DifferentPopulations

Table 44 shows the comparison of the immunogenicity, antigenicity, andeffectiveness of PolyPEPI1018 in different populations.

TABLE 44 Comparison of Immunogenicity, Antigenicity, and Effectivenessof PolyPEPI1018 in Different Sub-populations Number Number of Number ofNumber of of PEPI3+ AP AGP50 Populations subject Average SD Average SDAverage SD CRC 37 5.16 1.98 3.19 1.31 2.21 1.13 Model 433 5.02 2.62 3.621.67 2.54 1.25 Big 7,189 5.20 2.82 3.75 1.74 2.66 1.30 Chinese 324 5.973.16 4.28 1.78 3.11 1.30 Irish 999 3.72 1.92 2.86 1.46 1.94 1.10Abbreviations: CRC = colorectal cancer; PEPI = personal epitope; SD =standard deviation; AP = expressed antigens with ≥PEPI

The average number of PEPI3+ and AP results demonstrate thatPolyPEPI1018 is highly immunogenic and antigenic in all populations;PolyPEPI1018 can induce an average of 3.7-6.0 CRC specific T cell clonesagainst 2.9-3.7 CRC antigens. PolyPEPI1018 immunogenicity was similar inpatients with CRC and the average population (p>0.05), this similaritymay have been due to the small sample size of the CRC population.Additional analyses suggest that PolyPEPI1018 is significantly moreimmunogenic in a Chinese population compared to an Irish or a generalpopulation (p<0.0001). The differences in immunogenicity are alsoreflected in the effectiveness of the vaccine as characterized by AGP50;PolyPEPI1018 is most effective in a Chinese population and lesseffective in an Irish population. Since a CDx will be used to selectlikely responders to PolyPEPI1018, ethnic differences will only bereflected in the higher percentage of Chinese individuals that might beeligible for treatment compared with Irish individuals.

Example 24—Personalised Immunotherapy Composition for Treatment ofPatient with Late Stage Metastatic Breast Cancer

Patient BRC05 was diagnosed with inflammatory breast cancer on the rightwith extensive lymphangiosis carcinomatose. Inflammatory breast cancer(IBC) is a rare, but aggressive form of locally advanced breast cancer.It's called inflammatory breast cancer because its main symptoms areswelling and redness (the breast often looks inflamed). Mostinflammatory breast cancers are invasive ductal carcinomas (begin in themilk ducts). This type of breast cancer is associated with theexpression of oncoproteins of high risk Human Papilloma Virus. Indeed,HPV16 DNA was diagnosed in the tumor of this patient.

Patient's stage in 2011 (6 years prior to PIT vaccine treatment)

T4: Tumor of any size with direct extension to the chest wall and/or tothe skin (ulceration or skin nodules)pN3a: Metastases in ≥10 axillary lymph nodes (at least 1 tumordeposit >2.0 mm or metastases to the infraclavicular (level III axillarylymph) nodes.

14 vaccine peptides were designed and prepared for patient BRC05 (Table45). Peptides PBRC05-P01-P10 were made for this patient based onpopulation expression data. The last 3 peptides in the Table 45 (SSX-2,MORC, MAGE-B1) were designed from antigens that expression was measureddirectly in the tumor of the patient.

TABLE 45 Vaccine peptides for patient BRC05 BRCO5 vaccine Target AntigenMAXHLA MAXHLA peptides Antigen Expression 20mer peptide Class I Class IIPBRC05_P1 SPAG9 88% XXXXXXXXXXXXXXXXXXXX 3 4 PBRC05_P2 AKAP4 85%XXXXXXXXXXXXXXXXXXXX 3 4 PBRC05_P3 MAGE-All 59% XXXXXXXXXXXXXXXXXXXX 3 3PBRC05_P4 NY-SAR-35 49% XXXXXXXXXXXXXXXXXXXX 3 3 PBRC05_P5 FSIP1 49%XXXXXXXXXXXXXXXXXXXX 3 3 PBRC05_P6 NY-BR-1 47% XXXXXXXXXXXXXXXXXXXX 3 4PBRC05_P7 MAGE-A9 44% XXXXXXXXXXXXXXXXXXXX 3 3 PBRC05_P8 SCP-1 38%XXXXXXXXXXXXXXXXXXXX 3 6 PBRC05_P9 MAGE-A1 37% XXXXXXXXXXXXXXXXXXXX 3 3PBRC05_P10 MAGE-C2 21% XXXXXXXXXXXXXXXXXXXX 3 3 PBRC05_P11 MAGE-A12 13%XXXXXXXXXXXXXXXXXXXX 3 4 PBRC05_P12 SSX-2  6% XXXXXXXXXXXXXXXXXXXX 3 1PBRC05_P13 MORC ND XXXXXXXXXXXXXXXXXXXX 3 4 PBRC05_P14 MAGE-B1 NDXXXXXXXXXXXXXXXXXXXX 3 3 Note: Bold red means CD8 PEPI, Underline meansbest binding CD4 allele.

T cell responses were measured cells in peripheral mononuclear cells 2weeks after the Pt vaccination with the mix of peptides PBRC05_P1,PBRC05_P2, PBRC05_P3, PBRC05_P4, PBRC05_P5, PBRC05_P6, PBRC05_P7.

TABLE 46 Antigen specific T cell responses: Number of spots/300,000 PBMCAntigen Stimulant Exp1 Exp2 Average SPAG9 PBRC05_P1 2 1 1.5 AKAP4PBRC05_P2 11 4 7.5 MAGE-A11 PBRC05_P3 26 32 29 NY-SAR-35 PBRC05_P4 472497 484.5 FSIP1 PBRC05_P5 317 321 319 NY-BR-1 PBRC05_P6 8 12 10 MAGE-A9PBRC05_P7 23 27 25 None Negative Control (DMSO) 0 3 1.5

The results show that a single immunization with 7 peptides inducedpotent T cell responses against 3 out of the 7 peptides demonstratingpotent MAGE-A11, NY-SAR-35, FSIP1 and MAGE-A9 specific T cell responses.There were weak responses against AKAP4 and NY-BR-1 and no responseagainst SPAG9.

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What is claimed is:
 1. A pharmaceutical composition for treatment of adisease or disorder in a subject of a target human population,comprising one or more polypeptides, each comprising at least a firstregion and a second region, (a) the first region being of 10-50 aminoacids in length comprising a first amino acid sequence that is a T cellepitope that binds at least three HLA class I molecules of at least 10%of subjects in the target population and/or at least three HLA class IImolecules of at least 10% of subjects in the target population; and (b)the second region being of 10-50 amino acids in length comprising asecond amino acid sequence that is a T cell epitope that binds at leastthree HLA class I molecules of at least 10% of subjects in the targetpopulation and/or at least three HLA class II molecules of at least 10%of subjects in the target population; wherein the amino acid sequence ofthe T cell epitope of each of first and second regions comprisedifferent sequences.
 2. The pharmaceutical composition of claim 1,comprising at least 2, at least 3, at least 4, at least 5, at least 6,at least 7, at least 8, at least 9, at least 10, at least 11, or atleast 12 different polypeptides.
 3. The pharmaceutical composition ofclaim 1, comprising 2-40 different polypeptides.
 4. The pharmaceuticalcomposition of claim 1, wherein the T cell epitope that binds at leastthree HLA class I molecules of at least 10% of subjects in the targetpopulation comprises 7 to 11 amino acids, and/or the T cell epitope thatbinds at least three HLA class II molecules of at least 10% of subjectsin the target population comprises 13 to 17 amino acids.
 5. Thepharmaceutical composition of claim 1, wherein the first region of 10-50amino acids in length is from an antigen; and the second region of 10-50amino acids in length is from a same or different antigen.
 6. Thepharmaceutical composition of claim 1, wherein the epitopes of the firstand second regions are from a single antigen.
 7. The pharmaceuticalcomposition of claim 1, wherein the epitopes of the first and secondregions are from two or more different antigens.
 8. The pharmaceuticalcomposition of claim 5, wherein the antigen is a cancer-associatedantigen, a tumor-associated antigen, or an antigen expressed by a targetpathogenic organism, an antigen expressed by a virus, an antigenexpressed by a bacterium, an antigen expressed by a fungus, an antigenassociated with an autoimmune disorder, or is an allergen.
 9. Thepharmaceutical composition of claim 5, wherein the antigen is selectedfrom the antigens listed in Tables 2 to
 7. 10. The pharmaceuticalcomposition of claim 6, wherein the two or more different antigens areselected from the antigens listed in Tables 2 to 7 and/or differentcancer associated antigens.
 11. The pharmaceutical composition of claim9, wherein one or more of the antigens are cancer testis antigens(CTAs).
 12. The pharmaceutical composition of claim 1, wherein the oneor more polypeptides further comprise up to 10 amino acids flanking theT cell epitope that are not part of a consecutive sequence flanking theepitope in a corresponding antigen.
 13. The pharmaceutical compositionof claim 1, wherein the one or more polypeptides have been screened toeliminate substantially all neoepitopes that span a junction between thefirst region and second region and that (i) corresponds to a fragment ofa human polypeptide expressed in healthy cells; (ii) is a T cell epitopecapable of binding to at least three HLA class I molecules of at least10% of subjects in the target population; or (iii) meets bothrequirements (i) and (ii).
 14. The pharmaceutical composition of claim1, wherein the target population is cancer patients and wherein each ofthe first region and second region comprises an amino acid sequence thatis an HLA class I-binding T cell epitope, and wherein for each T cellepitope, (i) at least 10% of subjects in the target population express atumor associated antigen selected from the antigens listed in Table 2that comprises the T cell epitope; and (ii) at least 10% of subjects inthe target population have at least three HLA class I molecules capableof binding to the T cell epitope; wherein the T cell epitope of thefirst and second regions are different from each other.
 15. Thepharmaceutical composition of claim 1, further comprising apharmaceutically acceptable adjuvant, diluent, carrier, preservative, orcombination thereof.
 16. The pharmaceutical composition of claim 15,wherein the adjuvant is selected from the group consisting of MontanideISA-51, QS-21, GM-CSF, cyclophosamide, bacillus Calmette-Guerin (BCG),corynbacterium parvum, levamisole, azimezone, isoprinisone,dinitrochlorobenezene (DNCB), keyhole limpet hemocyanins (KLH), Freundsadjuvant (complete), Freunds adjuvant (incomplete), mineral gels,aluminum hydroxide (Alum), lysolecithin, pluronic polyols, polyanions,oil emulsions, dinitrophenol, diphtheria toxin (DT), and combinationsthereof.
 17. A kit comprising, one or more separate containers eachcontainer comprising: (i) one or more polypeptides comprising at least afirst region and a second region, (a) the first region of 10-50 aminoacids in length comprising a first amino acid sequence that is a T cellepitope that binds at least three HLA class I molecules of at least 10%of subjects in the target population and/or at least three HLA class IImolecules of at least 10% of subjects in the target population; and (b)the second region of 10-50 amino acids in length comprising a secondamino acid sequence that is a T cell epitope that binds at least threeHLA class I molecules of at least 10% of subjects in the targetpopulation and/or at least three HLA class II molecules of at least 10%of subjects in the target population; wherein the amino acid sequence ofthe T cell epitope of each of first and second regions comprisedifferent sequences and (ii) a pharmaceutically acceptable adjuvant,diluent, carrier, preservative, or combination thereof.
 18. The kit ofclaim 17, further comprising a package insert.
 19. A pharmaceuticalcomposition comprising: one or more nucleic acid molecules expressingone or more polypeptides comprising at least a first region and a secondregion, (a) the first region of 10-50 amino acids in length comprising afirst amino acid sequence that is a T cell epitope that binds at leastthree HLA class I molecules of at least 10% of subjects in the targetpopulation and/or at least three HLA class II molecules of at least 10%of subjects in the target population; and (b) the second region of 10-50amino acids in length comprising a second amino acid sequence that is aT cell epitope that binds at least three HLA class I molecules of atleast 10% of subjects in the target population and/or at least three HLAclass II molecules of at least 10% of subjects in the target population;wherein the amino acid sequence of the T cell epitope of each of firstand second regions comprise different sequences.
 20. A method ofpreparing a polypeptide, or a polynucleic acid that encodes apolypeptide, for use in a method of inducing an immune response in asubject of a target human population, the method comprising: (i)selecting: (a) a relevant model human population comprising a pluralityof subjects each defined by HLA class I genotype and/or by HLA class IIgenotype; or (b) one relevant model human population comprising aplurality of subjects each defined by HLA class I genotype and onerelevant model human population comprising a plurality of subjects eachdefined by HLA class II genotype; (ii) identifying a fragment of up to50 consecutive amino acids of an antigen that comprises: (a) a T cellepitope capable, in a high percentage of subjects of the modelpopulation selected in step (i) that is defined by HLA class I genotype,of binding to at least three HLA class I molecules of individualsubjects of the model population; (b) a T cell epitope capable, in ahigh percentage of subjects of the model population selected in step (i)that is defined by HLA class II genotype, of binding to at least threeHLA class II molecules of individual subjects of the model population;or (c) a T cell epitope capable, in a high percentage of subjects of themodel population selected in step (i) that is defined by HLA class Igenotype, of binding to at least three HLA class I molecules ofindividual subjects of the model population and a T cell epitopecapable, in a high percentage of subjects of the model populationselected in step (i) that is defined by HLA class II genotype, ofbinding to at least three HLA class II molecules of individual subjectsof the model population; and (iii) preparing a polypeptide, or apolynucleic acid that encodes a polypeptide that comprises one or morefragments identified in step (ii).
 21. The method of claim 20, furthercomprising prior to step (iii), selecting a longer fragment of theantigen if the fragment selected in step (ii) is an HLA class I—bindingepitope, which longer fragment comprises an amino acid sequence that (a)comprises the fragment selected in step (ii); and (b) is an HLA class IImolecule-binding T cell epitope capable, in a high percentage ofsubjects of the model population selected in step (i) that is defined byHLA class II genotype, of binding to at least three, or the mostpossible HLA class II molecules of individual subjects of the modelpopulation.
 22. The method of claim 20, further comprising prior to step(iii), repeating steps (i) to (ii) to identify on or more additionalamino acid sequences of up to 50 consecutive amino acids of the same ora different polypeptide to the first amino acid sequence.
 23. A methodof inducing an immune response in a subject of a target humanpopulation, the method comprising, administering to the subject apharmaceutical composition comprising one or more polypeptidescomprising at least a first region and a second region, (a) the firstregion being of 10-50 amino acids in length comprising a first aminoacid sequence that is a T cell epitope that binds at least three HLAclass I molecules of at least 10% of subjects in the target populationand/or at least three HLA class II molecules of at least 10% of subjectsin the target population; and (b) the second region being of 10-50 aminoacids in length comprising a second amino acid sequence that is a T cellepitope that binds at least three HLA class I molecules of at least 10%of subjects in the target population and/or at least three HLA class IImolecules of at least 10% of subjects in the target population; whereinthe amino acid sequence of the T cell epitope of each of first andsecond regions comprise different sequences.
 24. The method of claim 23,further comprising prior to the administering step, determining if thesubject is likely to have an have a clinical response to administrationof a pharmaceutical composition by (i) assaying a biological sample ofthe subject to determine HLA genotype of the subject; (ii) determiningthat the pharmaceutical composition comprises two or more sequences thatare a T cell epitope capable of binding to at least three HLA class Imolecules of the subject; and (iii) determining the probability that atumor of the subject expresses one or more antigen corresponding to theT cell epitopes identified in step (ii) using population expression datafor each antigen, to identify the likelihood of the subject to have aclinical response to administration of the pharmaceutical composition.25. The method of claim 23, wherein the first region of 10-50 aminoacids in length is from an antigen; and the second region of 10-50 aminoacids in length is from a same or different antigen.
 26. The method ofclaim 23, wherein the epitopes of the first and second regions are fromtwo or more different antigens.
 27. The method of claim 25, wherein theantigen is a cancer-associated antigen, a tumor-associated antigen, oran antigen expressed by a target pathogenic organism, an antigenexpressed by a virus, an antigen expressed by a bacterium, an antigenexpressed by a fungus, an antigen associated with an autoimmunedisorder, or is an allergen.
 28. The method of claim 23, wherein the Tcell epitope that binds at least three HLA class I molecules of at least10% of subjects in the target population comprises 7 to 11 amino acids,and/or the T cell epitope that binds at least three HLA class IImolecules of at least 10% of subjects in the target population comprises13 to 17 amino acids.
 29. A pharmaceutical composition for treatment ofa disease or disorder in a subject of a target human population,comprising (a) at least two polypeptides, each of the at least twopolypeptides being 10-50 amino acids in length comprising an amino acidsequence that is a T cell epitope that binds at least three HLA class Imolecules of at least 10% of subjects in the target population, and/orat least three HLA class II molecules of at least 10% of subjects in thetarget population, wherein the amino acid sequence of the T cell epitopeof each of the at least two polypeptides are different from each other;and (b) a pharmaceutically-acceptable adjuvant.
 30. The pharmaceuticalcomposition of claim 29, comprising at least 3, at least 4, at least 5,at least 6, at least 7, at least 8, at least 9, at least 10, at least11, or at least 12 different polypeptides.
 31. The pharmaceuticalcomposition of claim 29, comprising 3-40 different polypeptides.
 32. Thepharmaceutical composition of claim 29, wherein the T cell epitope thatbinds at least three HLA class I molecules of at least 10% of subjectsin the target population comprises 7 to 11 amino acids, and/or the Tcell epitope that binds at least three HLA class II molecules of atleast 10% of subjects in the target population comprises 13 to 17 aminoacids.
 33. The pharmaceutical composition of claim 29, wherein theepitopes of the amino acid sequences of the at least two polypeptidesare from a single antigen.
 34. The pharmaceutical composition of claim29, wherein the epitopes of the amino acid sequences of the at least twopolypeptides are from two or more different antigens.
 35. Thepharmaceutical composition of claim 33, wherein the antigen is acancer-associated antigen, a tumor-associated antigen, or an antigenexpressed by a target pathogenic organism, an antigen expressed by avirus, an antigen expressed by a bacterium, an antigen expressed by afungus, an antigen associated with an autoimmune disorder, or is anallergen.
 36. The pharmaceutical composition of claim 33, wherein theantigen is selected from the antigens listed in Tables 2 to
 7. 37. Thepharmaceutical composition of claim 34, wherein the two or moredifferent antigens are selected from the antigens listed in Tables 2 to7 and/or different cancer associated antigens.
 38. The pharmaceuticalcomposition of claim 37, wherein one or more of the antigens are cancertestis antigens (CTAs).
 39. The pharmaceutical composition of claim 29,wherein each of the at least two polypeptides being 10-50 amino acids inlength is from an antigen a same or different antigen.
 40. Thepharmaceutical composition of claim 29, wherein the at least twodifferent polypeptides further comprise up to 10 amino acids flankingthe T cell epitope that are not part of a consecutive sequence flankingthe epitope in a corresponding antigen.
 41. The pharmaceuticalcomposition of claim 29, wherein two of the at least two polypeptidesare arranged end to end or overlapping in a joined polypeptide.
 42. Thepharmaceutical composition of claim 41, comprising two or more differentjoined polypeptides, wherein the two or more different joinedpolypeptides comprise different epitopes from each other.
 43. Thepharmaceutical composition of claim 42, wherein the joined polypeptideshave been screened to eliminate substantially all neoepitopes that spana junction between the two polypeptides and that (i) corresponds to afragment of a human polypeptide expressed in healthy cells; (ii) is a Tcell epitope capable of binding to at least three HLA class I moleculesof at least 10% of subjects in the target population; or (iii) meetsboth requirements (i) and (ii).
 44. The pharmaceutical composition ofclaim 29, wherein the target population is cancer patients and whereineach polypeptide comprises an amino acid sequence that is an HLA classI-binding T cell epitope, and wherein for each T cell epitope, (i) atleast 10% of subjects in the target population express a tumorassociated antigen selected from the antigens listed in Table 2 thatcomprises the T cell epitope; and (ii) at least 10% of subjects in thetarget population have at least three HLA class I molecules capable ofbinding to the T cell epitope; wherein the T cell epitope of the atleast two polypeptides are different from each other.
 45. Thepharmaceutical composition of claim 29, further comprising apharmaceutically acceptable diluent, carrier, preservative, orcombination thereof.
 46. The pharmaceutical composition of claim 29,wherein the adjuvant is selected from the group consisting of MontanideISA-51, QS-21, GM-CSF, cyclophosamide, bacillus Calmette-Guerin (BCG),corynbacterium parvum, levamisole, azimezone, isoprinisone,dinitrochlorobenezene (DNCB), keyhole limpet hemocyanins (KLH), Freundsadjuvant (complete), Freunds adjuvant (incomplete), mineral gels,aluminum hydroxide (Alum), lysolecithin, pluronic polyols, polyanions,oil emulsions, dinitrophenol, diphtheria toxin (DT), and combinationsthereof.
 47. A pharmaceutical composition for treatment of a disease ordisorder in a subject of a target human population, comprising (a) apolypeptide of 10-50 amino acids in length and comprising a T cellepitope that binds at least three HLA class I molecules of at least 10%of subjects in the target population and/or at least three HLA class IImolecules of at least 10% of subjects in the target population; and (b)a pharmaceutically-acceptable adjuvant.
 48. The pharmaceuticalcomposition of claim 47, comprising at least 2, at least 3, at least 4,at least 5, at least 6, at least 7, at least 8, at least 9, at least 10,at least 11, or at least 12 different polypeptides, each of thedifferent polypeptides being 10-50 amino acids in length comprising a Tcell epitope that binds at least three HLA class I molecules of at least10% of subjects in the target population and/or at least three HLA classII molecules of at least 10% of subjects in the target population,wherein the amino acid sequence of the T cell epitope of each of thedifferent polypeptides are different from each other.
 49. Thepharmaceutical composition of claim 48, comprising 2-40 differentpolypeptides.
 50. The pharmaceutical composition of claim 47, whereinthe T cell epitope that binds at least three HLA class I molecules ofthe subject comprises 7 to 11 amino acids, and/or the T cell epitopethat binds at least three HLA class II molecules comprises 13 to 17amino acids.
 51. The pharmaceutical composition of claim 48, comprisingat least two different polypeptides, wherein the epitopes of the atleast two different polypeptides are from a single antigen.
 52. Thepharmaceutical composition of claim 48, comprising at least twodifferent polypeptides, wherein the epitopes of the at least twodifferent polypeptides are from two or more different antigens.
 53. Thepharmaceutical composition of claim 51, wherein the antigen is anantigen expressed by a cancer cell, a neoantigen expressed by a cancercell, a cancer-associated antigen, a tumor-associated antigen, or anantigen expressed by a target pathogenic organism, an antigen expressedby a virus, an antigen expressed by a bacterium, an antigen expressed bya fungus, an antigen associated with an autoimmune disorder, or is anallergen.
 54. The pharmaceutical composition of claim 51, wherein theantigen is selected from the antigens listed in Tables 2 to
 7. 55. Thepharmaceutical composition of claim 51, comprising at least twodifferent polypeptides, wherein two of the polypeptides are arranged endto end or overlapping in a joined polypeptide.
 56. The pharmaceuticalcomposition of claim 47, wherein the adjuvant is selected from the groupconsisting of Montanide ISA-51, QS-21, GM-CSF, cyclophosamide, bacillusCalmette-Guerin (BCG), corynbacterium parvum, levamisole, azimezone,isoprinisone, dinitrochlorobenezene (DNCB), keyhole limpet hemocyanins(KLH), Freunds adjuvant (complete), Freunds adjuvant (incomplete),mineral gels, aluminum hydroxide (Alum), lysolecithin, pluronic polyols,polyanions, oil emulsions, dinitrophenol, diphtheria toxin (DT), andcombinations thereof.
 57. The pharmaceutical composition of claim 47,comprising at least two different polypeptides, wherein two of the atleast two polypeptides are arranged end to end or overlapping in ajoined polypeptide.
 58. The pharmaceutical composition of claim 57,comprising two or more different joined polypeptides, wherein the two ormore different joined polypeptides comprise different epitopes from eachother.
 59. The pharmaceutical composition of claim 58, wherein thejoined polypeptides have been screened to eliminate substantially allneoepitopes that span a junction between the two polypeptides and that(i) corresponds to a fragment of a human polypeptide expressed inhealthy cells of the subject; (ii) is a T cell epitope capable ofbinding to at least two HLA class I molecules of the subject; or (iii)meets both requirements (i) and (ii).
 60. The pharmaceutical compositionof claim 48, wherein the at least two polypeptides do not comprise anyamino acid sequences that (i) correspond to a fragment of a humanpolypeptide expressed in healthy cells; or (ii) correspond to a fragmentof a human polypeptide expressed in healthy cells and is a T cellepitope capable of binding to at least two HLA class I molecules of thesubject.
 61. A method of identifying and treating a subject of a targetpopulation of cancer patients who will likely have a clinical responseto administration of a pharmaceutical composition according to claim 1,the method comprising, (i) assaying a biological sample of the subjectto determine HLA genotype of the subject; (ii) determining that thepharmaceutical composition comprises two or more sequences that are a Tcell epitope capable of binding to at least three HLA class I moleculesof the subject; (iii) determining the probability that a tumor of thesubject expresses one or more antigen corresponding to the T cellepitopes identified in step (ii) using population expression data foreach antigen, to identify the likelihood of the subject to have aclinical response to administration of the pharmaceutical composition;and (iv) administering the composition of claim 1 to the identifiedsubject.
 62. The method of claim 61, further comprising prior to theadministering step assaying a tumor sample from the subject to determinethat the three or more peptides of the pharmaceutical compositioncomprise two or more different amino acid sequences each of which is a.a fragment of a cancer-associated antigen expressed by cancer cells ofthe subject as determined in step (i); and b. a T cell epitope capableof binding to at least three HLA class I molecules of the subject; andconfirming the subject as likely to have a clinical response to themethod of treatment.
 63. The method of claim 61, wherein the compositioncomprises at least 2, at least 3, at least 4, at least 5, at least 6, atleast 7, at least 8, at least 9, at least 10, at least 11, or at least12 different polypeptides.
 64. The method of claim 61, wherein thecomposition comprises 2-40 different polypeptides.
 65. The method ofclaim 61, wherein the T cell epitope that binds at least three HLA classI molecules of at least 10% of subjects in the target populationcomprises 7 to 11 amino acids, and/or the T cell epitope that binds atleast three HLA class II molecules of at least 10% of subjects in thetarget population comprises 13 to 17 amino acids.
 66. The method ofclaim 61, wherein the first region of 10-50 amino acids in length isfrom an antigen; and the second region of 10-50 amino acids in length isfrom a same or different antigen.
 67. The method of claim 61, whereinthe epitopes of the first and second regions are from a single antigen.68. The method of claim 61, wherein the epitopes of the first and secondregions are from two or more different antigens.
 69. The method of claim67, wherein the antigen is a cancer-associated antigen or atumor-associated antigen.
 70. The method of claim 67, wherein theantigen is selected from the antigens listed in Table
 2. 71. The methodof claim 67, wherein the two or more different antigens are selectedfrom the antigens listed in Table 2 and/or different cancer associatedantigens.
 72. The method of claim 71, wherein one or more of theantigens are cancer testis antigens (CTAs).
 73. The method of claim 61,wherein the one or more polypeptides further comprise up to 10 aminoacids flanking the T cell epitope that are not part of a consecutivesequence flanking the epitope in a corresponding antigen.
 74. The methodof claim 61, wherein the one or more polypeptides have been screened toeliminate substantially all neoepitopes that span a junction between thefirst region and second region and that (i) corresponds to a fragment ofa human polypeptide expressed in healthy cells; (ii) is a T cell epitopecapable of binding to at least three HLA class I molecules of at least10% of subjects in the target population; or (iii) meets bothrequirements (i) and (ii).
 75. The method of claim 61, wherein thetarget population is cancer patients and wherein each of the firstregion and second region comprises an amino acid sequence that is an HLAclass I-binding T cell epitope, and wherein for each T cell epitope,(iii) at least 10% of subjects in the target population express a tumorassociated antigen selected from the antigens listed in Table 2 thatcomprises the T cell epitope; and (iv) at least 10% of subjects in thetarget population have at least three HLA class I molecules capable ofbinding to the T cell epitope; wherein the T cell epitope of the firstand second regions are different from each other.
 76. The method ofclaim 61, wherein the composition further comprises a pharmaceuticallyacceptable adjuvant, diluent, carrier, preservative, or combinationthereof.
 77. The method of claim 61, wherein the adjuvant is selectedfrom the group consisting of Montanide ISA-51, QS-21, GM-CSF,cyclophosamide, bacillus Calmette-Guerin (BCG), corynbacterium parvum,levamisole, azimezone, isoprinisone, dinitrochlorobenezene (DNCB),keyhole limpet hemocyanins (KLH), Freunds adjuvant (complete), Freundsadjuvant (incomplete), mineral gels, aluminum hydroxide (Alum),lysolecithin, pluronic polyols, polyanions, oil emulsions,dinitrophenol, diphtheria toxin (DT), and combinations thereof.
 78. Akit comprising: (a) a first composition comprising (i) a firstpolypeptide of 10-50 amino acids in length and comprising a T cellepitope that binds at least three HLA class I molecules of at least 10%of subjects in the target population and/or at least three HLA class IImolecules of at least 10% of subjects in the target population; and (ii)a pharmaceutically-acceptable adjuvant; (b) a second compositioncomprising (i) a second polypeptide of 10-50 amino acids in length andcomprising a T cell epitope that binds at least three HLA class Imolecules of at least 10% of subjects in the target population and/or atleast three HLA class II molecules of at least 10% of subjects in thetarget population; and (ii) a pharmaceutically-acceptable adjuvant,wherein the first and second polypeptides comprise different T cellepitopes.
 79. The kit of claim 78, wherein the first composition and/orthe second composition comprise one or more additional polypeptides,wherein each additional polypeptide being of 10-50 amino acids in lengthcomprising an amino acid sequence that is a T cell epitope that binds atleast three HLA class I molecules of at least 10% of subjects in thetarget population and/or at least three HLA class II molecules of atleast 10% of subjects in the target population, wherein the amino acidsequences comprise different T cell epitopes.
 80. A method ofidentifying and treating a subject of a target population of cancerpatients who will likely have an immune response to administration of apharmaceutical composition according to claim 1, the method comprising,(i) assaying a biological sample of the subject to determine HLAgenotype of the subject; (ii) determining that the pharmaceuticalcomposition comprises two or more sequences that are a T cell epitopecapable of binding to at least three HLA class I molecules of thesubject; (iii) administering the composition of claim 1 to theidentified subject.
 81. A pharmaceutical composition comprising: anucleic acid molecule expressing two or more polypeptides, eachpolypeptide being 10-50 amino acids in length comprising a T cellepitope that binds at least three HLA class I molecules of at least 10%of subjects in the target population and/or at least three HLA class IImolecules of at least 10% of subjects in the target population, whereineach of the two or more polypeptides comprises a different T cellepitope, wherein the polypeptides do not comprise amino acid sequencesthat are adjacent to each other in a corresponding antigen.